diff --git a/src/workflows/post_processing/config.vsh.yaml b/src/workflows/post_processing/config.vsh.yaml index 50b52e9..fa6fe56 100644 --- a/src/workflows/post_processing/config.vsh.yaml +++ b/src/workflows/post_processing/config.vsh.yaml @@ -151,6 +151,8 @@ dependencies: - name: samtools/samtools_idxstats repository: biobox - name: stringtie + # - name: bedtools/bedtools_genomecov + # repository: biobox - name: bedtools_genomecov - name: ucsc/bedclip - name: ucsc/bedgraphtobigwig diff --git a/src/workflows/pre_processing/config.vsh.yaml b/src/workflows/pre_processing/config.vsh.yaml index 1438c25..f3e8686 100644 --- a/src/workflows/pre_processing/config.vsh.yaml +++ b/src/workflows/pre_processing/config.vsh.yaml @@ -246,7 +246,20 @@ argument_groups: direction: output description: Results from Salmon quant default: $id.salmon_quant_output - + - name: --trim_json + type: file + description: The fastp json format report file name + default: $id.fastp_out.json + direction: output + - name: --trim_html + type: file + description: The fastp html format report file name + default: $id.fastp_out.html + direction: output + - name: --merged_out + type: file + description: File name to store merged fastp output. + direction: output resources: - type: nextflow_script path: main.nf diff --git a/src/workflows/quality_control/config.vsh.yaml b/src/workflows/quality_control/config.vsh.yaml index 072d347..c39d2a7 100644 --- a/src/workflows/quality_control/config.vsh.yaml +++ b/src/workflows/quality_control/config.vsh.yaml @@ -600,27 +600,27 @@ argument_groups: - name: "--pseudo_tpm_gene" type: file direction: output - default: salmon.merged.pseudo_gene_tpm.tsv + default: pseudo_gene_tpm.tsv - name: "--pseudo_counts_gene" type: file direction: output - default: salmon.merged.pseudo_gene_counts.tsv + default: pseudo_gene_counts.tsv - name: "--pseudo_counts_gene_length_scaled" type: file direction: output - default: salmon.merged.pseudo_gene_counts_length_scaled.tsv + default: pseudo_gene_counts_length_scaled.tsv - name: "--pseudo_counts_gene_scaled" type: file direction: output - default: salmon.merged.pseudo_gene_counts_scaled.tsv + default: pseudo_gene_counts_scaled.tsv - name: "--pseudo_tpm_transcript" type: file direction: output - default: salmon.merged.pseudo_transcript_tpm.tsv + default: pseudo_transcript_tpm.tsv - name: "--pseudo_counts_transcript" type: file direction: output - default: salmon.merged.pseudo_transcript_counts.tsv + default: pseudo_transcript_counts.tsv - name: "--pseudo_quant_merged_summarizedexperiment" type: file direction: output @@ -642,6 +642,8 @@ dependencies: - name: rseqc/rseqc_tin - name: dupradar - name: qualimap + # - name: qualimap/qualimap_rnaseq + # repository: biobox - name: preseq_lcextrap - name: featurecounts repository: biobox diff --git a/src/workflows/rnaseq/config.vsh.yaml b/src/workflows/rnaseq/config.vsh.yaml index 1541a8e..05fcb40 100644 --- a/src/workflows/rnaseq/config.vsh.yaml +++ b/src/workflows/rnaseq/config.vsh.yaml @@ -435,6 +435,16 @@ argument_groups: required: false must_exist: false default: trimgalore/$id.read_2.trimming_report.txt + - name: --fastp_trim_json + type: file + description: The fastp json format report file name + default: fastp/$id_out.json + direction: output + - name: --fastp_trim_html + type: file + description: The fastp html format report file name + default: fastp/$id_out.html + direction: output - name: "--trim_html_1" type: file direction: output @@ -513,35 +523,35 @@ argument_groups: - name: "--salmon_quant_results" type: file direction: output - default: salmon/$id + default: alignment_quantification/$id - name: "--tpm_gene" type: file direction: output - default: salmon/gene_tpm.tsv + default: alignment_quantification/gene_tpm.tsv - name: "--counts_gene" type: file direction: output - default: salmon/gene_counts.tsv + default: alignment_quantification/gene_counts.tsv - name: "--counts_gene_length_scaled" type: file direction: output - default: salmon/gene_counts_length_scaled.tsv + default: alignment_quantification/gene_counts_length_scaled.tsv - name: "--counts_gene_scaled" type: file direction: output - default: salmon/gene_counts_scaled.tsv + default: alignment_quantification/gene_counts_scaled.tsv - name: "--tpm_transcript" type: file direction: output - default: salmon/transcript_tpm.tsv + default: alignment_quantification/transcript_tpm.tsv - name: "--counts_transcript" type: file direction: output - default: salmon/transcript_counts.tsv + default: alignment_quantification/transcript_counts.tsv - name: "--salmon_merged_summarizedexperiment" type: file direction: output - default: salmon/summarizedexperiment + default: alignment_quantification/summarizedexperiment - name: "--markduplicates_metrics" type: file direction: output @@ -813,7 +823,31 @@ argument_groups: type: file must_exist: false direction: output - + - name: "--pseudo_counts_gene" + type: file + direction: output + default: pseudo_alignment_quantification/gene_counts.tsv + - name: "--pseudo_counts_gene_length_scaled" + type: file + direction: output + default: pseudo_alignment_quantification/gene_counts_length_scaled.tsv + - name: "--pseudo_counts_gene_scaled" + type: file + direction: output + default: pseudo_alignment_quantification/gene_counts_scaled.tsv + - name: "--pseudo_tpm_transcript" + type: file + direction: output + default: pseudo_alignment_quantification/transcript_tpm.tsv + - name: "--pseudo_counts_transcript" + type: file + direction: output + default: pseudo_alignment_quantification/transcript_counts.tsv + - name: "--pseudo_quant_merged_summarizedexperiment" + type: file + direction: output + default: pseudo_alignment_quantification/quant_merged_summarizedexperiment + resources: - type: nextflow_script path: main.nf diff --git a/src/workflows/rnaseq/main.nf b/src/workflows/rnaseq/main.nf index 3b416cd..6c56290 100644 --- a/src/workflows/rnaseq/main.nf +++ b/src/workflows/rnaseq/main.nf @@ -230,7 +230,11 @@ workflow run_wf { "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", "transcriptome_bam_idxstats": "transcriptome_bam_idxstats", "quant_out_dir": "quant_out_dir", - "quant_results_file": "quant_results_file" + "quant_results_file": "quant_results_file", + "rsem_counts_gene": "rsem_counts_gene", + "rsem_counts_transcripts": "rsem_counts_transcripts", + "bam_genome_rsem": "bam_genome_rsem", + "bam_transcript_rsem": "bam_transcript_rsem" ] ) diff --git a/target/executable/bbmap_bbsplit/.config.vsh.yaml b/target/executable/bbmap_bbsplit/.config.vsh.yaml index 1140c62..579642f 100644 --- a/target/executable/bbmap_bbsplit/.config.vsh.yaml +++ b/target/executable/bbmap_bbsplit/.config.vsh.yaml @@ -238,8 +238,8 @@ build_info: output: "target/executable/bbmap_bbsplit" executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/bbmap_bbsplit/bbmap_bbsplit b/target/executable/bbmap_bbsplit/bbmap_bbsplit index 69edcc9..6835aa9 100755 --- a/target/executable/bbmap_bbsplit/bbmap_bbsplit +++ b/target/executable/bbmap_bbsplit/bbmap_bbsplit @@ -506,9 +506,9 @@ tar xzf BBMap_39.01.tar.gz && \ cp -r bbmap/* /usr/local/bin LABEL org.opencontainers.image.description="Companion container for running component bbmap_bbsplit" -LABEL org.opencontainers.image.created="2024-09-23T10:27:04Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:49:53Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools_genomecov/.config.vsh.yaml index 5f730af..17de6b9 100644 --- a/target/executable/bedtools_genomecov/.config.vsh.yaml +++ b/target/executable/bedtools_genomecov/.config.vsh.yaml @@ -178,8 +178,8 @@ build_info: output: "target/executable/bedtools_genomecov" executable: "target/executable/bedtools_genomecov/bedtools_genomecov" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools_genomecov/bedtools_genomecov index 2910da0..46d13f5 100755 --- a/target/executable/bedtools_genomecov/bedtools_genomecov +++ b/target/executable/bedtools_genomecov/bedtools_genomecov @@ -481,9 +481,9 @@ mv bedtools.static /usr/local/bin/bedtools && \ chmod a+x /usr/local/bin/bedtools LABEL org.opencontainers.image.description="Companion container for running component bedtools_genomecov" -LABEL org.opencontainers.image.created="2024-09-23T10:27:04Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:49:54Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/cat_additional_fasta/.config.vsh.yaml b/target/executable/cat_additional_fasta/.config.vsh.yaml index d3558ca..b3184e6 100644 --- a/target/executable/cat_additional_fasta/.config.vsh.yaml +++ b/target/executable/cat_additional_fasta/.config.vsh.yaml @@ -182,8 +182,8 @@ build_info: output: "target/executable/cat_additional_fasta" executable: "target/executable/cat_additional_fasta/cat_additional_fasta" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/cat_additional_fasta/cat_additional_fasta b/target/executable/cat_additional_fasta/cat_additional_fasta index 3eb5dac..3c6876b 100755 --- a/target/executable/cat_additional_fasta/cat_additional_fasta +++ b/target/executable/cat_additional_fasta/cat_additional_fasta @@ -480,9 +480,9 @@ function ViashDockerfile { FROM python:latest ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component cat_additional_fasta" -LABEL org.opencontainers.image.created="2024-09-23T10:27:12Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:00Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/cat_fastq/.config.vsh.yaml b/target/executable/cat_fastq/.config.vsh.yaml index 29472ed..a749477 100644 --- a/target/executable/cat_fastq/.config.vsh.yaml +++ b/target/executable/cat_fastq/.config.vsh.yaml @@ -169,8 +169,8 @@ build_info: output: "target/executable/cat_fastq" executable: "target/executable/cat_fastq/cat_fastq" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/cat_fastq/cat_fastq b/target/executable/cat_fastq/cat_fastq index cef68de..5c12290 100755 --- a/target/executable/cat_fastq/cat_fastq +++ b/target/executable/cat_fastq/cat_fastq @@ -472,9 +472,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component cat_fastq" -LABEL org.opencontainers.image.created="2024-09-23T10:27:13Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:01Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/deseq2_qc/.config.vsh.yaml b/target/executable/deseq2_qc/.config.vsh.yaml index 1fb25d4..31247c1 100644 --- a/target/executable/deseq2_qc/.config.vsh.yaml +++ b/target/executable/deseq2_qc/.config.vsh.yaml @@ -237,8 +237,8 @@ build_info: output: "target/executable/deseq2_qc" executable: "target/executable/deseq2_qc/deseq2_qc" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/deseq2_qc/deseq2_qc b/target/executable/deseq2_qc/deseq2_qc index 6641855..3e4db20 100755 --- a/target/executable/deseq2_qc/deseq2_qc +++ b/target/executable/deseq2_qc/deseq2_qc @@ -502,9 +502,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag Rscript -e 'remotes::install_url(c("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc" -LABEL org.opencontainers.image.created="2024-09-23T10:27:22Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:10Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/dupradar/.config.vsh.yaml b/target/executable/dupradar/.config.vsh.yaml index 82e4e2e..0808ca6 100644 --- a/target/executable/dupradar/.config.vsh.yaml +++ b/target/executable/dupradar/.config.vsh.yaml @@ -266,8 +266,8 @@ build_info: output: "target/executable/dupradar" executable: "target/executable/dupradar/dupradar" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/dupradar/dupradar b/target/executable/dupradar/dupradar index 810ab82..6a866d2 100755 --- a/target/executable/dupradar/dupradar +++ b/target/executable/dupradar/dupradar @@ -520,9 +520,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa Rscript -e 'if (!requireNamespace("dupRadar", quietly = TRUE)) BiocManager::install("dupRadar")' LABEL org.opencontainers.image.description="Companion container for running component dupradar" -LABEL org.opencontainers.image.created="2024-09-23T10:27:14Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:02Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml index 1835e7b..ecb7d0e 100644 --- a/target/executable/fastqc/.config.vsh.yaml +++ b/target/executable/fastqc/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/executable/fastqc" executable: "target/executable/fastqc/fastqc" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc index bf1fa54..0fa02ee 100755 --- a/target/executable/fastqc/fastqc +++ b/target/executable/fastqc/fastqc @@ -490,9 +490,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component fastqc" -LABEL org.opencontainers.image.created="2024-09-23T10:27:05Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:49:55Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/fq_subsample/.config.vsh.yaml b/target/executable/fq_subsample/.config.vsh.yaml index 7da70f2..20fe951 100644 --- a/target/executable/fq_subsample/.config.vsh.yaml +++ b/target/executable/fq_subsample/.config.vsh.yaml @@ -177,8 +177,8 @@ build_info: output: "target/executable/fq_subsample" executable: "target/executable/fq_subsample/fq_subsample" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/fq_subsample/fq_subsample b/target/executable/fq_subsample/fq_subsample index 905c823..5a1ca0e 100755 --- a/target/executable/fq_subsample/fq_subsample +++ b/target/executable/fq_subsample/fq_subsample @@ -485,9 +485,9 @@ cargo install --locked --path . && \ mv /usr/local/fq/target/release/fq /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component fq_subsample" -LABEL org.opencontainers.image.created="2024-09-23T10:27:05Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:49:55Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/getchromsizes/.config.vsh.yaml b/target/executable/getchromsizes/.config.vsh.yaml index dc74a87..0b4163e 100644 --- a/target/executable/getchromsizes/.config.vsh.yaml +++ b/target/executable/getchromsizes/.config.vsh.yaml @@ -167,8 +167,8 @@ build_info: output: "target/executable/getchromsizes" executable: "target/executable/getchromsizes/getchromsizes" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/getchromsizes/getchromsizes b/target/executable/getchromsizes/getchromsizes index 5bac749..70fa79e 100755 --- a/target/executable/getchromsizes/getchromsizes +++ b/target/executable/getchromsizes/getchromsizes @@ -480,9 +480,9 @@ make && \ make install LABEL org.opencontainers.image.description="Companion container for running component getchromsizes" -LABEL org.opencontainers.image.created="2024-09-23T10:27:05Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:49:56Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/gtf2bed/.config.vsh.yaml b/target/executable/gtf2bed/.config.vsh.yaml index c3d4f20..7172c9a 100644 --- a/target/executable/gtf2bed/.config.vsh.yaml +++ b/target/executable/gtf2bed/.config.vsh.yaml @@ -145,8 +145,8 @@ build_info: output: "target/executable/gtf2bed" executable: "target/executable/gtf2bed/gtf2bed" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/gtf2bed/gtf2bed b/target/executable/gtf2bed/gtf2bed index 8cb423c..cc3816e 100755 --- a/target/executable/gtf2bed/gtf2bed +++ b/target/executable/gtf2bed/gtf2bed @@ -466,9 +466,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component gtf2bed" -LABEL org.opencontainers.image.created="2024-09-23T10:27:18Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:06Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/gtf_filter/.config.vsh.yaml b/target/executable/gtf_filter/.config.vsh.yaml index 33dd712..cd7110c 100644 --- a/target/executable/gtf_filter/.config.vsh.yaml +++ b/target/executable/gtf_filter/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/executable/gtf_filter" executable: "target/executable/gtf_filter/gtf_filter" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/gtf_filter/gtf_filter b/target/executable/gtf_filter/gtf_filter index 7ea13f9..2441110 100755 --- a/target/executable/gtf_filter/gtf_filter +++ b/target/executable/gtf_filter/gtf_filter @@ -470,9 +470,9 @@ function ViashDockerfile { FROM python:latest ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component gtf_filter" -LABEL org.opencontainers.image.created="2024-09-23T10:27:21Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:09Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/gunzip/.config.vsh.yaml b/target/executable/gunzip/.config.vsh.yaml index 3d5d985..2ca803b 100644 --- a/target/executable/gunzip/.config.vsh.yaml +++ b/target/executable/gunzip/.config.vsh.yaml @@ -144,8 +144,8 @@ build_info: output: "target/executable/gunzip" executable: "target/executable/gunzip/gunzip" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/gunzip/gunzip b/target/executable/gunzip/gunzip index b44ef24..1d31a95 100755 --- a/target/executable/gunzip/gunzip +++ b/target/executable/gunzip/gunzip @@ -466,9 +466,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component gunzip" -LABEL org.opencontainers.image.created="2024-09-23T10:27:06Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:49:56Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_index/.config.vsh.yaml b/target/executable/kallisto/kallisto_index/.config.vsh.yaml index 811c4c8..3a2be56 100644 --- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/executable/kallisto/kallisto_index" executable: "target/executable/kallisto/kallisto_index/kallisto_index" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/kallisto/kallisto_index/kallisto_index b/target/executable/kallisto/kallisto_index/kallisto_index index aa70464..3f5adc8 100755 --- a/target/executable/kallisto/kallisto_index/kallisto_index +++ b/target/executable/kallisto/kallisto_index/kallisto_index @@ -471,9 +471,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \ mv kallisto/kallisto /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index" -LABEL org.opencontainers.image.created="2024-09-23T10:27:19Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:07Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml index 42dc3c5..9fec34d 100644 --- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/executable/kallisto/kallisto_quant" executable: "target/executable/kallisto/kallisto_quant/kallisto_quant" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/kallisto/kallisto_quant/kallisto_quant b/target/executable/kallisto/kallisto_quant/kallisto_quant index 21cf6fc..4cbaead 100755 --- a/target/executable/kallisto/kallisto_quant/kallisto_quant +++ b/target/executable/kallisto/kallisto_quant/kallisto_quant @@ -515,9 +515,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \ mv kallisto/kallisto /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant" -LABEL org.opencontainers.image.created="2024-09-23T10:27:19Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:07Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/multiqc_custom_biotype/.config.vsh.yaml b/target/executable/multiqc_custom_biotype/.config.vsh.yaml index 7bc9f16..8832176 100644 --- a/target/executable/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/executable/multiqc_custom_biotype/.config.vsh.yaml @@ -170,8 +170,8 @@ build_info: output: "target/executable/multiqc_custom_biotype" executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype index 8e2c440..232a9fd 100755 --- a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype +++ b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype @@ -481,9 +481,9 @@ RUN apt-get update && \ RUN pip install --upgrade pip LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype" -LABEL org.opencontainers.image.created="2024-09-23T10:27:14Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:02Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/picard_markduplicates/.config.vsh.yaml b/target/executable/picard_markduplicates/.config.vsh.yaml index 0e4f3cd..92d8732 100644 --- a/target/executable/picard_markduplicates/.config.vsh.yaml +++ b/target/executable/picard_markduplicates/.config.vsh.yaml @@ -207,8 +207,8 @@ build_info: output: "target/executable/picard_markduplicates" executable: "target/executable/picard_markduplicates/picard_markduplicates" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/picard_markduplicates/picard_markduplicates b/target/executable/picard_markduplicates/picard_markduplicates index 9af6ec0..4078329 100755 --- a/target/executable/picard_markduplicates/picard_markduplicates +++ b/target/executable/picard_markduplicates/picard_markduplicates @@ -494,9 +494,9 @@ wget --no-check-certificate https://github.com/broadinstitute/picard/releases/do mv picard.jar /usr/local/bin LABEL org.opencontainers.image.description="Companion container for running component picard_markduplicates" -LABEL org.opencontainers.image.created="2024-09-23T10:27:21Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:09Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/prepare_multiqc_input/.config.vsh.yaml b/target/executable/prepare_multiqc_input/.config.vsh.yaml index 197d101..633eef9 100644 --- a/target/executable/prepare_multiqc_input/.config.vsh.yaml +++ b/target/executable/prepare_multiqc_input/.config.vsh.yaml @@ -409,8 +409,8 @@ build_info: output: "target/executable/prepare_multiqc_input" executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/prepare_multiqc_input/prepare_multiqc_input b/target/executable/prepare_multiqc_input/prepare_multiqc_input index 20715a6..3f7021f 100755 --- a/target/executable/prepare_multiqc_input/prepare_multiqc_input +++ b/target/executable/prepare_multiqc_input/prepare_multiqc_input @@ -557,9 +557,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input" -LABEL org.opencontainers.image.created="2024-09-23T10:27:17Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:05Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml index 4d2fd0c..bc8c56d 100644 --- a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml +++ b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml @@ -138,8 +138,8 @@ build_info: output: "target/executable/preprocess_transcripts_fasta" executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta index e3c1c6d..23e850e 100755 --- a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta +++ b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta @@ -462,9 +462,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component preprocess_transcripts_fasta" -LABEL org.opencontainers.image.created="2024-09-23T10:27:17Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:05Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/preseq_lcextrap/.config.vsh.yaml b/target/executable/preseq_lcextrap/.config.vsh.yaml index 8507af7..73580d1 100644 --- a/target/executable/preseq_lcextrap/.config.vsh.yaml +++ b/target/executable/preseq_lcextrap/.config.vsh.yaml @@ -191,8 +191,8 @@ build_info: output: "target/executable/preseq_lcextrap" executable: "target/executable/preseq_lcextrap/preseq_lcextrap" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/preseq_lcextrap/preseq_lcextrap b/target/executable/preseq_lcextrap/preseq_lcextrap index 649ee8c..add8e49 100755 --- a/target/executable/preseq_lcextrap/preseq_lcextrap +++ b/target/executable/preseq_lcextrap/preseq_lcextrap @@ -495,9 +495,9 @@ mkdir build && cd build && \ make && make install && make HAVE_HTSLIB=1 all LABEL org.opencontainers.image.description="Companion container for running component preseq_lcextrap" -LABEL org.opencontainers.image.created="2024-09-23T10:27:06Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:49:56Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/qualimap/.config.vsh.yaml b/target/executable/qualimap/.config.vsh.yaml index 7e7e16f..9130050 100644 --- a/target/executable/qualimap/.config.vsh.yaml +++ b/target/executable/qualimap/.config.vsh.yaml @@ -271,8 +271,8 @@ build_info: output: "target/executable/qualimap" executable: "target/executable/qualimap/qualimap" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/qualimap/qualimap b/target/executable/qualimap/qualimap index 29cd9d4..4ba0c40 100755 --- a/target/executable/qualimap/qualimap +++ b/target/executable/qualimap/qualimap @@ -537,9 +537,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag Rscript -e 'remotes::install_cran(c("optparse"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.description="Companion container for running component qualimap" -LABEL org.opencontainers.image.created="2024-09-23T10:27:04Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:49:54Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml index a3237c2..d5ba3ec 100644 --- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -299,8 +299,8 @@ build_info: output: "target/executable/rsem/rsem_calculate_expression" executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression index ed623ee..1dac580 100755 --- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression +++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression @@ -542,9 +542,9 @@ echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \ /bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR" LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression" -LABEL org.opencontainers.image.created="2024-09-23T10:27:19Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:07Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml index b9d3cdf..baefb9b 100644 --- a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml @@ -202,8 +202,8 @@ build_info: output: "target/executable/rsem/rsem_merge_counts" executable: "target/executable/rsem/rsem_merge_counts/rsem_merge_counts" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts index 47b2910..aae4e33 100755 --- a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts +++ b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts @@ -490,9 +490,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_merge_counts" -LABEL org.opencontainers.image.created="2024-09-23T10:27:18Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:06Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml index fca6c8e..9e676d9 100644 --- a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -163,8 +163,8 @@ build_info: output: "target/executable/rseqc/rseqc_bamstat" executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat index 854389a..8033d7a 100755 --- a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat +++ b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat @@ -477,9 +477,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat" -LABEL org.opencontainers.image.created="2024-09-23T10:27:16Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:04Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml index 2ad98b1..e3b81df 100644 --- a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -186,8 +186,8 @@ build_info: output: "target/executable/rseqc/rseqc_inferexperiment" executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment index 7a0dabf..0fc9da0 100755 --- a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment +++ b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment @@ -487,9 +487,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment" -LABEL org.opencontainers.image.created="2024-09-23T10:27:14Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:02Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml index 3857b59..bf024f4 100644 --- a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml @@ -272,8 +272,8 @@ build_info: output: "target/executable/rseqc/rseqc_innerdistance" executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance index 564f772..ba86f03 100755 --- a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance +++ b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance @@ -529,9 +529,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_innerdistance" -LABEL org.opencontainers.image.created="2024-09-23T10:27:16Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:04Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml index e75b219..b335b41 100644 --- a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml @@ -260,8 +260,8 @@ build_info: output: "target/executable/rseqc/rseqc_junctionannotation" executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation index 5ad2494..78e7275 100755 --- a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation +++ b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation @@ -519,9 +519,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionannotation" -LABEL org.opencontainers.image.created="2024-09-23T10:27:16Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:04Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index ef863e8..97fa846 100644 --- a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml @@ -249,8 +249,8 @@ build_info: output: "target/executable/rseqc/rseqc_junctionsaturation" executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation b/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation index e7335d4..a9ac6ed 100755 --- a/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation +++ b/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation @@ -522,9 +522,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionsaturation" -LABEL org.opencontainers.image.created="2024-09-23T10:27:15Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:03Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml index 201ea5b..18b5822 100644 --- a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml @@ -162,8 +162,8 @@ build_info: output: "target/executable/rseqc/rseqc_readdistribution" executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution b/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution index 13696f8..c7f6b90 100755 --- a/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution +++ b/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution @@ -474,9 +474,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readdistribution" -LABEL org.opencontainers.image.created="2024-09-23T10:27:16Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:04Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml index 90a3671..8ea0edf 100644 --- a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml @@ -211,8 +211,8 @@ build_info: output: "target/executable/rseqc/rseqc_readduplication" executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication b/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication index 06a2aa1..503a790 100755 --- a/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication +++ b/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication @@ -499,9 +499,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readduplication" -LABEL org.opencontainers.image.created="2024-09-23T10:27:15Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:03Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml index 2705d17..db67e8a 100644 --- a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml @@ -214,8 +214,8 @@ build_info: output: "target/executable/rseqc/rseqc_tin" executable: "target/executable/rseqc/rseqc_tin/rseqc_tin" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_tin/rseqc_tin b/target/executable/rseqc/rseqc_tin/rseqc_tin index e61016a..cb7266a 100755 --- a/target/executable/rseqc/rseqc_tin/rseqc_tin +++ b/target/executable/rseqc/rseqc_tin/rseqc_tin @@ -501,9 +501,9 @@ RUN apt-get update && \ RUN pip3 install RSeQC LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_tin" -LABEL org.opencontainers.image.created="2024-09-23T10:27:15Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:03Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml index 1e6029d..8d0f3ab 100644 --- a/target/executable/sortmerna/.config.vsh.yaml +++ b/target/executable/sortmerna/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/executable/sortmerna" executable: "target/executable/sortmerna/sortmerna" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna index b960c83..75032d9 100755 --- a/target/executable/sortmerna/sortmerna +++ b/target/executable/sortmerna/sortmerna @@ -492,9 +492,9 @@ wget --no-check-certificate https://github.com/sortmerna/sortmerna/releases/down bash sortmerna-4.3.6-Linux.sh --skip-license LABEL org.opencontainers.image.description="Companion container for running component sortmerna" -LABEL org.opencontainers.image.created="2024-09-23T10:27:21Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:09Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/stringtie/.config.vsh.yaml b/target/executable/stringtie/.config.vsh.yaml index f837934..6f1ece0 100644 --- a/target/executable/stringtie/.config.vsh.yaml +++ b/target/executable/stringtie/.config.vsh.yaml @@ -216,8 +216,8 @@ build_info: output: "target/executable/stringtie" executable: "target/executable/stringtie/stringtie" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/stringtie/stringtie b/target/executable/stringtie/stringtie index 6ceba3c..ed90380 100755 --- a/target/executable/stringtie/stringtie +++ b/target/executable/stringtie/stringtie @@ -496,9 +496,9 @@ tar -xzf stringtie-2.2.1.Linux_x86_64.tar.gz && \ cp stringtie-2.2.1.Linux_x86_64/stringtie /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component stringtie" -LABEL org.opencontainers.image.created="2024-09-23T10:27:18Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:06Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/summarizedexperiment/.config.vsh.yaml b/target/executable/summarizedexperiment/.config.vsh.yaml index 52646fe..5374b4b 100644 --- a/target/executable/summarizedexperiment/.config.vsh.yaml +++ b/target/executable/summarizedexperiment/.config.vsh.yaml @@ -199,8 +199,8 @@ build_info: output: "target/executable/summarizedexperiment" executable: "target/executable/summarizedexperiment/summarizedexperiment" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/summarizedexperiment/summarizedexperiment b/target/executable/summarizedexperiment/summarizedexperiment index 38f2211..1aecb09 100755 --- a/target/executable/summarizedexperiment/summarizedexperiment +++ b/target/executable/summarizedexperiment/summarizedexperiment @@ -487,9 +487,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa Rscript -e 'if (!requireNamespace("tximeta", quietly = TRUE)) BiocManager::install("tximeta")' LABEL org.opencontainers.image.description="Companion container for running component summarizedexperiment" -LABEL org.opencontainers.image.created="2024-09-23T10:27:22Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:10Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/trimgalore/.config.vsh.yaml b/target/executable/trimgalore/.config.vsh.yaml index 2a253de..c15222b 100644 --- a/target/executable/trimgalore/.config.vsh.yaml +++ b/target/executable/trimgalore/.config.vsh.yaml @@ -788,8 +788,8 @@ build_info: output: "target/executable/trimgalore" executable: "target/executable/trimgalore/trimgalore" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/trimgalore/trimgalore b/target/executable/trimgalore/trimgalore index 9da0fbf..c9bdbaa 100755 --- a/target/executable/trimgalore/trimgalore +++ b/target/executable/trimgalore/trimgalore @@ -858,9 +858,9 @@ ENTRYPOINT [] RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component trimgalore" -LABEL org.opencontainers.image.created="2024-09-23T10:27:20Z" +LABEL org.opencontainers.image.created="2024-09-23T13:50:08Z" LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/tx2gene/.config.vsh.yaml b/target/executable/tx2gene/.config.vsh.yaml index 1fc7de7..59ae741 100644 --- a/target/executable/tx2gene/.config.vsh.yaml +++ b/target/executable/tx2gene/.config.vsh.yaml @@ -192,8 +192,8 @@ build_info: output: "target/executable/tx2gene" executable: "target/executable/tx2gene/tx2gene" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/tx2gene/tx2gene b/target/executable/tx2gene/tx2gene index 70c1018..4f94f9c 100755 --- a/target/executable/tx2gene/tx2gene +++ b/target/executable/tx2gene/tx2gene @@ -487,9 +487,9 @@ RUN apt-get update && \ RUN pip install --upgrade pip LABEL org.opencontainers.image.description="Companion container for running component tx2gene" -LABEL org.opencontainers.image.created="2024-09-23T10:27:17Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:05Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/tximport/.config.vsh.yaml b/target/executable/tximport/.config.vsh.yaml index 4c721c2..5cc5dd7 100644 --- a/target/executable/tximport/.config.vsh.yaml +++ b/target/executable/tximport/.config.vsh.yaml @@ -247,8 +247,8 @@ build_info: output: "target/executable/tximport" executable: "target/executable/tximport/tximport" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/tximport/tximport b/target/executable/tximport/tximport index f099dea..d3e2c0a 100755 --- a/target/executable/tximport/tximport +++ b/target/executable/tximport/tximport @@ -508,9 +508,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag Rscript -e 'remotes::install_cran(c("jsonlite"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.description="Companion container for running component tximport" -LABEL org.opencontainers.image.created="2024-09-23T10:27:12Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:00Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/ucsc/bedclip/.config.vsh.yaml b/target/executable/ucsc/bedclip/.config.vsh.yaml index ec69217..bc49bf2 100644 --- a/target/executable/ucsc/bedclip/.config.vsh.yaml +++ b/target/executable/ucsc/bedclip/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/executable/ucsc/bedclip" executable: "target/executable/ucsc/bedclip/bedclip" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/ucsc/bedclip/bedclip b/target/executable/ucsc/bedclip/bedclip index f0da78b..fb3e36d 100755 --- a/target/executable/ucsc/bedclip/bedclip +++ b/target/executable/ucsc/bedclip/bedclip @@ -473,9 +473,9 @@ RUN apt-get update && \ RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedClip /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component ucsc bedclip" -LABEL org.opencontainers.image.created="2024-09-23T10:27:13Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:01Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml index fb8fcb9..73ef84d 100644 --- a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml +++ b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/executable/ucsc/bedgraphtobigwig" executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig b/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig index dfc6ba2..68015c5 100755 --- a/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig +++ b/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig @@ -473,9 +473,9 @@ RUN apt-get update && \ RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component ucsc bedgraphtobigwig" -LABEL org.opencontainers.image.created="2024-09-23T10:27:13Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:01Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/umitools/umitools_dedup/.config.vsh.yaml b/target/executable/umitools/umitools_dedup/.config.vsh.yaml index 44e3ead..9203148 100644 --- a/target/executable/umitools/umitools_dedup/.config.vsh.yaml +++ b/target/executable/umitools/umitools_dedup/.config.vsh.yaml @@ -195,8 +195,8 @@ build_info: output: "target/executable/umitools/umitools_dedup" executable: "target/executable/umitools/umitools_dedup/umitools_dedup" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/umitools/umitools_dedup/umitools_dedup b/target/executable/umitools/umitools_dedup/umitools_dedup index 924e729..ceb6c15 100755 --- a/target/executable/umitools/umitools_dedup/umitools_dedup +++ b/target/executable/umitools/umitools_dedup/umitools_dedup @@ -489,9 +489,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "umi_tools" LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_dedup" -LABEL org.opencontainers.image.created="2024-09-23T10:27:20Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:08Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/umitools/umitools_extract/.config.vsh.yaml b/target/executable/umitools/umitools_extract/.config.vsh.yaml index a215d1a..9d3ec1b 100644 --- a/target/executable/umitools/umitools_extract/.config.vsh.yaml +++ b/target/executable/umitools/umitools_extract/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/executable/umitools/umitools_extract" executable: "target/executable/umitools/umitools_extract/umitools_extract" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/umitools/umitools_extract/umitools_extract b/target/executable/umitools/umitools_extract/umitools_extract index 3df2b4e..929c971 100755 --- a/target/executable/umitools/umitools_extract/umitools_extract +++ b/target/executable/umitools/umitools_extract/umitools_extract @@ -521,9 +521,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "umi_tools" LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_extract" -LABEL org.opencontainers.image.created="2024-09-23T10:27:20Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:08Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/umitools_prepareforquant/.config.vsh.yaml b/target/executable/umitools_prepareforquant/.config.vsh.yaml index b46e4eb..f60c12e 100644 --- a/target/executable/umitools_prepareforquant/.config.vsh.yaml +++ b/target/executable/umitools_prepareforquant/.config.vsh.yaml @@ -156,8 +156,8 @@ build_info: output: "target/executable/umitools_prepareforquant" executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/umitools_prepareforquant/umitools_prepareforquant b/target/executable/umitools_prepareforquant/umitools_prepareforquant index 6311a9e..8577ae1 100755 --- a/target/executable/umitools_prepareforquant/umitools_prepareforquant +++ b/target/executable/umitools_prepareforquant/umitools_prepareforquant @@ -473,9 +473,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "umi_tools" "pysam" LABEL org.opencontainers.image.description="Companion container for running component umitools_prepareforquant" -LABEL org.opencontainers.image.created="2024-09-23T10:27:22Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" +LABEL org.opencontainers.image.created="2024-09-23T13:50:10Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml b/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml index 4650796..af6bd18 100644 --- a/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -596,8 +596,8 @@ build_info: output: "target/executable/workflows/genome_alignment_and_quant" executable: "target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" diff --git a/target/executable/workflows/merge_quant_results/.config.vsh.yaml b/target/executable/workflows/merge_quant_results/.config.vsh.yaml index 7d39bf3..2e0643d 100644 --- a/target/executable/workflows/merge_quant_results/.config.vsh.yaml +++ b/target/executable/workflows/merge_quant_results/.config.vsh.yaml @@ -278,8 +278,8 @@ build_info: output: "target/executable/workflows/merge_quant_results" executable: "target/executable/workflows/merge_quant_results/merge_quant_results" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/tx2gene" - "target/nextflow/tximport" diff --git a/target/executable/workflows/post_processing/.config.vsh.yaml b/target/executable/workflows/post_processing/.config.vsh.yaml index 5416376..6936af7 100644 --- a/target/executable/workflows/post_processing/.config.vsh.yaml +++ b/target/executable/workflows/post_processing/.config.vsh.yaml @@ -486,8 +486,8 @@ build_info: output: "target/executable/workflows/post_processing" executable: "target/executable/workflows/post_processing/post_processing" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" diff --git a/target/executable/workflows/pre_processing/.config.vsh.yaml b/target/executable/workflows/pre_processing/.config.vsh.yaml index 309adbd..9b83b05 100644 --- a/target/executable/workflows/pre_processing/.config.vsh.yaml +++ b/target/executable/workflows/pre_processing/.config.vsh.yaml @@ -510,6 +510,40 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" + - type: "file" + name: "--trim_json" + description: "The fastp json format report file name" + info: null + default: + - "$id.fastp_out.json" + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--trim_html" + description: "The fastp html format report file name" + info: null + default: + - "$id.fastp_out.html" + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--merged_out" + description: "File name to store merged fastp output." + info: null + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" resources: - type: "nextflow_script" path: "main.nf" @@ -639,8 +673,8 @@ build_info: output: "target/executable/workflows/pre_processing" executable: "target/executable/workflows/pre_processing/pre_processing" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/fastqc" - "target/nextflow/umitools/umitools_extract" diff --git a/target/executable/workflows/pre_processing/pre_processing b/target/executable/workflows/pre_processing/pre_processing index 8a3d41c..d89842b 100755 --- a/target/executable/workflows/pre_processing/pre_processing +++ b/target/executable/workflows/pre_processing/pre_processing @@ -411,6 +411,20 @@ function ViashHelp { echo " type: file, output, file must exist" echo " default: \$id.salmon_quant_output" echo " Results from Salmon quant" + echo "" + echo " --trim_json" + echo " type: file, output, file must exist" + echo " default: \$id.fastp_out.json" + echo " The fastp json format report file name" + echo "" + echo " --trim_html" + echo " type: file, output, file must exist" + echo " default: \$id.fastp_out.html" + echo " The fastp html format report file name" + echo "" + echo " --merged_out" + echo " type: file, output, file must exist" + echo " File name to store merged fastp output." } # initialise variables @@ -925,6 +939,39 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_SALMON_QUANT_OUTPUT=$(ViashRemoveFlags "$1") shift 1 ;; + --trim_json) + [ -n "$VIASH_PAR_TRIM_JSON" ] && ViashError Bad arguments for option \'--trim_json\': \'$VIASH_PAR_TRIM_JSON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_TRIM_JSON="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --trim_json. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --trim_json=*) + [ -n "$VIASH_PAR_TRIM_JSON" ] && ViashError Bad arguments for option \'--trim_json=*\': \'$VIASH_PAR_TRIM_JSON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_TRIM_JSON=$(ViashRemoveFlags "$1") + shift 1 + ;; + --trim_html) + [ -n "$VIASH_PAR_TRIM_HTML" ] && ViashError Bad arguments for option \'--trim_html\': \'$VIASH_PAR_TRIM_HTML\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_TRIM_HTML="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --trim_html. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --trim_html=*) + [ -n "$VIASH_PAR_TRIM_HTML" ] && ViashError Bad arguments for option \'--trim_html=*\': \'$VIASH_PAR_TRIM_HTML\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_TRIM_HTML=$(ViashRemoveFlags "$1") + shift 1 + ;; + --merged_out) + [ -n "$VIASH_PAR_MERGED_OUT" ] && ViashError Bad arguments for option \'--merged_out\': \'$VIASH_PAR_MERGED_OUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MERGED_OUT="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --merged_out. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --merged_out=*) + [ -n "$VIASH_PAR_MERGED_OUT" ] && ViashError Bad arguments for option \'--merged_out=*\': \'$VIASH_PAR_MERGED_OUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_MERGED_OUT=$(ViashRemoveFlags "$1") + shift 1 + ;; ---engine) VIASH_ENGINE_ID="$2" shift 2 @@ -1161,6 +1208,12 @@ fi if [ -z ${VIASH_PAR_SALMON_QUANT_OUTPUT+x} ]; then VIASH_PAR_SALMON_QUANT_OUTPUT="\$id.salmon_quant_output" fi +if [ -z ${VIASH_PAR_TRIM_JSON+x} ]; then + VIASH_PAR_TRIM_JSON="\$id.fastp_out.json" +fi +if [ -z ${VIASH_PAR_TRIM_HTML+x} ]; then + VIASH_PAR_TRIM_HTML="\$id.fastp_out.html" +fi # check whether required files exist if [ ! -z "$VIASH_PAR_FASTQ_1" ] && [ ! -e "$VIASH_PAR_FASTQ_1" ]; then @@ -1430,6 +1483,15 @@ fi if [ ! -z "$VIASH_PAR_SALMON_QUANT_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_SALMON_QUANT_OUTPUT")" ]; then mkdir -p "$(dirname "$VIASH_PAR_SALMON_QUANT_OUTPUT")" fi +if [ ! -z "$VIASH_PAR_TRIM_JSON" ] && [ ! -d "$(dirname "$VIASH_PAR_TRIM_JSON")" ]; then + mkdir -p "$(dirname "$VIASH_PAR_TRIM_JSON")" +fi +if [ ! -z "$VIASH_PAR_TRIM_HTML" ] && [ ! -d "$(dirname "$VIASH_PAR_TRIM_HTML")" ]; then + mkdir -p "$(dirname "$VIASH_PAR_TRIM_HTML")" +fi +if [ ! -z "$VIASH_PAR_MERGED_OUT" ] && [ ! -d "$(dirname "$VIASH_PAR_MERGED_OUT")" ]; then + mkdir -p "$(dirname "$VIASH_PAR_MERGED_OUT")" +fi if [ "$VIASH_ENGINE_ID" == "native" ] ; then if [ "$VIASH_MODE" == "run" ]; then @@ -1724,6 +1786,18 @@ if [ ! -z "$VIASH_PAR_SALMON_QUANT_OUTPUT" ] && [ ! -e "$VIASH_PAR_SALMON_QUANT_ ViashError "Output file '$VIASH_PAR_SALMON_QUANT_OUTPUT' does not exist." exit 1 fi +if [ ! -z "$VIASH_PAR_TRIM_JSON" ] && [ ! -e "$VIASH_PAR_TRIM_JSON" ]; then + ViashError "Output file '$VIASH_PAR_TRIM_JSON' does not exist." + exit 1 +fi +if [ ! -z "$VIASH_PAR_TRIM_HTML" ] && [ ! -e "$VIASH_PAR_TRIM_HTML" ]; then + ViashError "Output file '$VIASH_PAR_TRIM_HTML' does not exist." + exit 1 +fi +if [ ! -z "$VIASH_PAR_MERGED_OUT" ] && [ ! -e "$VIASH_PAR_MERGED_OUT" ]; then + ViashError "Output file '$VIASH_PAR_MERGED_OUT' does not exist." + exit 1 +fi exit 0 diff --git a/target/executable/workflows/prepare_genome/.config.vsh.yaml b/target/executable/workflows/prepare_genome/.config.vsh.yaml index 0657acb..d6cc5b4 100644 --- a/target/executable/workflows/prepare_genome/.config.vsh.yaml +++ b/target/executable/workflows/prepare_genome/.config.vsh.yaml @@ -496,8 +496,8 @@ build_info: output: "target/executable/workflows/prepare_genome" executable: "target/executable/workflows/prepare_genome/prepare_genome" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread" diff --git a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml index f3b2720..29ac8cc 100644 --- a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -285,8 +285,8 @@ build_info: output: "target/executable/workflows/pseudo_alignment_and_quant" executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" - "target/nextflow/kallisto/kallisto_quant" diff --git a/target/executable/workflows/quality_control/.config.vsh.yaml b/target/executable/workflows/quality_control/.config.vsh.yaml index 85fba38..0339a41 100644 --- a/target/executable/workflows/quality_control/.config.vsh.yaml +++ b/target/executable/workflows/quality_control/.config.vsh.yaml @@ -1367,7 +1367,7 @@ argument_groups: name: "--pseudo_tpm_gene" info: null default: - - "salmon.merged.pseudo_gene_tpm.tsv" + - "pseudo_gene_tpm.tsv" must_exist: true create_parent: true required: false @@ -1378,7 +1378,7 @@ argument_groups: name: "--pseudo_counts_gene" info: null default: - - "salmon.merged.pseudo_gene_counts.tsv" + - "pseudo_gene_counts.tsv" must_exist: true create_parent: true required: false @@ -1389,7 +1389,7 @@ argument_groups: name: "--pseudo_counts_gene_length_scaled" info: null default: - - "salmon.merged.pseudo_gene_counts_length_scaled.tsv" + - "pseudo_gene_counts_length_scaled.tsv" must_exist: true create_parent: true required: false @@ -1400,7 +1400,7 @@ argument_groups: name: "--pseudo_counts_gene_scaled" info: null default: - - "salmon.merged.pseudo_gene_counts_scaled.tsv" + - "pseudo_gene_counts_scaled.tsv" must_exist: true create_parent: true required: false @@ -1411,7 +1411,7 @@ argument_groups: name: "--pseudo_tpm_transcript" info: null default: - - "salmon.merged.pseudo_transcript_tpm.tsv" + - "pseudo_transcript_tpm.tsv" must_exist: true create_parent: true required: false @@ -1422,7 +1422,7 @@ argument_groups: name: "--pseudo_counts_transcript" info: null default: - - "salmon.merged.pseudo_transcript_counts.tsv" + - "pseudo_transcript_counts.tsv" must_exist: true create_parent: true required: false @@ -1592,8 +1592,8 @@ build_info: output: "target/executable/workflows/quality_control" executable: "target/executable/workflows/quality_control/quality_control" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/rseqc/rseqc_bamstat" - "target/nextflow/rseqc/rseqc_inferexperiment" diff --git a/target/executable/workflows/quality_control/quality_control b/target/executable/workflows/quality_control/quality_control index 5792065..cc61a9f 100755 --- a/target/executable/workflows/quality_control/quality_control +++ b/target/executable/workflows/quality_control/quality_control @@ -780,27 +780,27 @@ function ViashHelp { echo "" echo " --pseudo_tpm_gene" echo " type: file, output, file must exist" - echo " default: salmon.merged.pseudo_gene_tpm.tsv" + echo " default: pseudo_gene_tpm.tsv" echo "" echo " --pseudo_counts_gene" echo " type: file, output, file must exist" - echo " default: salmon.merged.pseudo_gene_counts.tsv" + echo " default: pseudo_gene_counts.tsv" echo "" echo " --pseudo_counts_gene_length_scaled" echo " type: file, output, file must exist" - echo " default: salmon.merged.pseudo_gene_counts_length_scaled.tsv" + echo " default: pseudo_gene_counts_length_scaled.tsv" echo "" echo " --pseudo_counts_gene_scaled" echo " type: file, output, file must exist" - echo " default: salmon.merged.pseudo_gene_counts_scaled.tsv" + echo " default: pseudo_gene_counts_scaled.tsv" echo "" echo " --pseudo_tpm_transcript" echo " type: file, output, file must exist" - echo " default: salmon.merged.pseudo_transcript_tpm.tsv" + echo " default: pseudo_transcript_tpm.tsv" echo "" echo " --pseudo_counts_transcript" echo " type: file, output, file must exist" - echo " default: salmon.merged.pseudo_transcript_counts.tsv" + echo " default: pseudo_transcript_counts.tsv" echo "" echo " --pseudo_quant_merged_summarizedexperiment" echo " type: file, output, file must exist" @@ -2704,22 +2704,22 @@ if [ -z ${VIASH_PAR_QUANT_MERGED_SUMMARIZEDEXPERIMENT+x} ]; then VIASH_PAR_QUANT_MERGED_SUMMARIZEDEXPERIMENT="salmon_merged_summarizedexperiment" fi if [ -z ${VIASH_PAR_PSEUDO_TPM_GENE+x} ]; then - VIASH_PAR_PSEUDO_TPM_GENE="salmon.merged.pseudo_gene_tpm.tsv" + VIASH_PAR_PSEUDO_TPM_GENE="pseudo_gene_tpm.tsv" fi if [ -z ${VIASH_PAR_PSEUDO_COUNTS_GENE+x} ]; then - VIASH_PAR_PSEUDO_COUNTS_GENE="salmon.merged.pseudo_gene_counts.tsv" + VIASH_PAR_PSEUDO_COUNTS_GENE="pseudo_gene_counts.tsv" fi if [ -z ${VIASH_PAR_PSEUDO_COUNTS_GENE_LENGTH_SCALED+x} ]; then - VIASH_PAR_PSEUDO_COUNTS_GENE_LENGTH_SCALED="salmon.merged.pseudo_gene_counts_length_scaled.tsv" + VIASH_PAR_PSEUDO_COUNTS_GENE_LENGTH_SCALED="pseudo_gene_counts_length_scaled.tsv" fi if [ -z ${VIASH_PAR_PSEUDO_COUNTS_GENE_SCALED+x} ]; then - VIASH_PAR_PSEUDO_COUNTS_GENE_SCALED="salmon.merged.pseudo_gene_counts_scaled.tsv" + VIASH_PAR_PSEUDO_COUNTS_GENE_SCALED="pseudo_gene_counts_scaled.tsv" fi if [ -z ${VIASH_PAR_PSEUDO_TPM_TRANSCRIPT+x} ]; then - VIASH_PAR_PSEUDO_TPM_TRANSCRIPT="salmon.merged.pseudo_transcript_tpm.tsv" + VIASH_PAR_PSEUDO_TPM_TRANSCRIPT="pseudo_transcript_tpm.tsv" fi if [ -z ${VIASH_PAR_PSEUDO_COUNTS_TRANSCRIPT+x} ]; then - VIASH_PAR_PSEUDO_COUNTS_TRANSCRIPT="salmon.merged.pseudo_transcript_counts.tsv" + VIASH_PAR_PSEUDO_COUNTS_TRANSCRIPT="pseudo_transcript_counts.tsv" fi if [ -z ${VIASH_PAR_PSEUDO_QUANT_MERGED_SUMMARIZEDEXPERIMENT+x} ]; then VIASH_PAR_PSEUDO_QUANT_MERGED_SUMMARIZEDEXPERIMENT="pseudo_quant_merged_summarizedexperiment" diff --git a/target/executable/workflows/rnaseq/.config.vsh.yaml b/target/executable/workflows/rnaseq/.config.vsh.yaml deleted file mode 100644 index 8125d0e..0000000 --- a/target/executable/workflows/rnaseq/.config.vsh.yaml +++ /dev/null @@ -1,1991 +0,0 @@ -name: "rnaseq" -namespace: "workflows" -version: "multiple_fixes" -argument_groups: -- name: "Input" - arguments: - - type: "string" - name: "--id" - description: "ID of the sample." - info: null - example: - - "foo" - required: true - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--fastq_1" - description: "Path to the sample (or read 1 of paired end sample)." - info: null - must_exist: true - create_parent: true - required: true - direction: "input" - multiple: true - multiple_sep: ";" - - type: "file" - name: "--fastq_2" - description: "Path to read 2 of the sample." - info: null - must_exist: false - create_parent: true - required: false - direction: "input" - multiple: true - multiple_sep: ";" - - type: "string" - name: "--strandedness" - description: "Sample strand-specificity. Must be one of unstranded, forward, reverse\ - \ or auto" - info: null - default: - - "auto" - required: false - choices: - - "unstranded" - - "forward" - - "reverse" - - "auto" - direction: "input" - multiple: false - multiple_sep: ";" -- name: "Reference genome options" - arguments: - - type: "file" - name: "--fasta" - description: "Path to FASTA genome file." - info: null - must_exist: true - create_parent: true - required: true - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--gtf" - description: "Path to GTF annotation file. This parameter is *mandatory* if --genome\ - \ is not specified." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--gff" - description: "Path to GFF3 annotation file. Required if \"--gtf\" is not specified." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--additional_fasta" - description: "FASTA file to concatenate to genome FASTA file e.g. containing spike-in\ - \ sequences." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--transcript_fasta" - description: "Path to FASTA transcriptome file." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--gene_bed" - description: "Path to BED file containing gene intervals. This will be created\ - \ from the GTF file if not specified." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--splicesites" - description: "Splice sites file required for HISAT2." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--star_index" - description: "Path to directory or tar.gz archive for pre-built STAR index." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--rsem_index" - description: "Path to directory or tar.gz archive for pre-built RSEM index." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--salmon_index" - description: "Path to directory or tar.gz archive for pre-built Salmon index." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--kallisto_index" - description: "Path to directory or tar.gz archive for pre-built Kallisto index." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean_true" - name: "--gencode" - description: "Specify if the GTF annotation is in GENCODE format." - info: null - direction: "input" - - type: "string" - name: "--gtf_extra_attributes" - description: "Additional gene identifiers from the input GTF file when running\ - \ Salmon. More than one value can be specified separated by comma." - info: null - default: - - "gene_name" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--gtf_group_features" - description: "Define the attribute type used to group features in the GTF file\ - \ when running Salmon." - info: null - default: - - "gene_id" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--featurecounts_group_type" - description: "The attribute type used to group feature types in the GTF file when\ - \ generating the biotype plot with featureCounts." - info: null - default: - - "gene_biotype" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--featurecounts_feature_type" - description: "By default, the pipeline assigns reads based on the 'exon' attribute\ - \ within the GTF file." - info: null - default: - - "exon" - required: false - direction: "input" - multiple: false - multiple_sep: ";" -- name: "Read trimming options" - arguments: - - type: "string" - name: "--trimmer" - description: "Specify the trimming tool to use." - info: null - default: - - "trimgalore" - required: false - choices: - - "trimgalore" - - "fastp" - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--extra_trimgalore_args" - description: "Extra arguments to pass to Trim Galore! command in addition to defaults\ - \ defined by the pipeline." - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--extra_fastp_args" - description: "Extra arguments to pass to fastp command in addition to defaults\ - \ defined by the pipeline." - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "integer" - name: "--min_trimmed_reads" - description: "Minimum number of trimmed reads below which samples are removed\ - \ from further processing. Some downstream steps in the pipeline will fail if\ - \ this threshold is too low." - info: null - default: - - 10000 - required: false - direction: "input" - multiple: false - multiple_sep: ";" -- name: "Read filtering options" - arguments: - - type: "file" - name: "--bbsplit_fasta_list" - description: "Path to comma-separated file containing a list of reference genomes\ - \ to filter reads against with BBSplit. To use BBSplit, \"--skip_bbsplit\" must\ - \ be explicitly set to \"false\". The file should contain 2 (comma separated)\ - \ columns - short name and full path to reference genome(s)" - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--bbsplit_index" - description: "Path to directory or tar.gz archive for pre-built BBSplit index." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean_true" - name: "--remove_ribo_rna" - description: "Enable the removal of reads derived from ribosomal RNA using SortMeRNA." - info: null - direction: "input" - - type: "file" - name: "--ribo_database_manifest" - description: "Text file containing paths to fasta files (one per line) that will\ - \ be used to create the database for SortMeRNA." - info: null - default: - - "assets/rrna-db-defaults.txt" - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" -- name: "UMI options" - arguments: - - type: "boolean_true" - name: "--with_umi" - description: "Enable UMI-based read deduplication." - info: null - direction: "input" - - type: "string" - name: "--umitools_extract_method" - description: "UMI pattern to use." - info: null - default: - - "string" - required: false - choices: - - "string" - - "regex" - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--umitools_bc_pattern" - description: "The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the\ - \ first 6 nucleotides of the read are from the UMI." - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--umitools_bc_pattern2" - description: "The UMI barcode pattern to use if the UMI is located in read 2." - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "integer" - name: "--umi_discard_read" - description: "After UMI barcode extraction discard either R1 or R2 by setting\ - \ this parameter to 1 or 2, respectively." - info: null - default: - - 0 - required: false - choices: - - 0 - - 1 - - 2 - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--umitools_umi_separator" - description: "The character that separates the UMI in the read name. Most likely\ - \ a colon if you skipped the extraction with UMI-tools and used other software." - info: null - default: - - "_" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--umitools_grouping_method" - description: "Method to use to determine read groups by subsuming those with similar\ - \ UMIs. All methods start by identifying the reads with the same mapping position,\ - \ but treat similar yet nonidentical UMIs differently." - info: null - default: - - "directional" - required: false - choices: - - "unique" - - "percentile" - - "cluster" - - "adjacency" - - "directional" - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean_true" - name: "--umi_dedup_stats" - description: "Generate output stats when running \"umi_tools dedup\"." - info: null - direction: "input" -- name: "Alignment options" - arguments: - - type: "string" - name: "--aligner" - description: "Specifies the alignment algorithm to use - available options are\ - \ 'star_salmon', 'star_rsem' and 'hisat2'." - info: null - default: - - "star_salmon" - required: false - choices: - - "star_salmon" - - "star_rsem" - - "hisat2" - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--pseudo_aligner" - description: "Specifies the pseudo aligner to use - available options are 'salmon'.\ - \ Runs in addition to '--aligner'." - info: null - default: - - "salmon" - required: false - choices: - - "salmon" - - "kallisto" - direction: "input" - multiple: false - multiple_sep: ";" - - type: "integer" - name: "--pseudo_aligner_kmer_size" - description: "Kmer length passed to indexing step of pseudoaligners." - info: null - default: - - 31 - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "integer" - name: "--kallisto_quant_fragment_length" - description: "For single-end mode only, the estimated average fragment length\ - \ to use for quantification with Kallisto." - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "integer" - name: "--kallisto_quant_fragment_length_sd" - description: "For single-end mode only, the estimated standard deviation of the\ - \ fragment length for quantification with Kallisto." - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean_true" - name: "--bam_csi_index" - description: "Create a CSI index for BAM files instead of the traditional BAI\ - \ index. This will be required for genomes with larger chromosome sizes." - info: null - direction: "input" - - type: "string" - name: "--salmon_quant_libtype" - description: "Override Salmon library type inferred based on strandedness defined\ - \ in meta object." - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--extra_salmon_quant_args" - description: "Extra arguments to pass to salmon quant command in addition to defaults\ - \ defined by the pipeline." - info: null - default: - - "-v" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "integer" - name: "--min_mapped_reads" - description: "Minimum percentage of uniquely mapped reads below which samples\ - \ are removed from further processing." - info: null - default: - - 5 - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean_true" - name: "--stringtie_ignore_gtf" - description: "Perform reference-guided de novo assembly of transcripts using StringTie,\ - \ i.e. don't restrict to those in GTF file." - info: null - direction: "input" - - type: "string" - name: "--extra_stringtie_args" - description: "Extra arguments to pass to stringtie command in addition to defaults\ - \ defined by the pipeline." - info: null - default: - - "-v" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean_true" - name: "--save_unaligned" - description: "Where possible, save unaligned reads from either STAR, HISAT2 or\ - \ Salmon to the results directory." - info: null - direction: "input" - - type: "boolean_true" - name: "--save_align_intermeds" - description: "Save the intermediate BAM files from the alignment step." - info: null - direction: "input" - - type: "boolean_true" - name: "--skip_alignment" - description: "Skip all of the alignment-based processes within the pipeline." - info: null - direction: "input" - - type: "boolean_true" - name: "--skip_pseudo_alignment" - description: "Skip all of the pseudo-alignment-based processes within the pipeline." - info: null - direction: "input" - - type: "string" - name: "--extra_rsem_calculate_expression_args" - description: "Extra arguments to pass to rsem-calculate-expression command in\ - \ addition to defaults defined by the pipeline." - info: null - default: - - "--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed\ - \ 1" - required: false - direction: "input" - multiple: false - multiple_sep: ";" -- name: "Process skipping options" - arguments: - - type: "boolean" - name: "--skip_fastqc" - description: "Skip FatQC step." - info: null - default: - - false - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean" - name: "--skip_trimming" - description: "Skip the adapter trimming step." - info: null - default: - - false - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean_true" - name: "--skip_bbsplit" - description: "Skip BBSplit for removal of non-reference genome reads." - info: null - direction: "input" - - type: "boolean" - name: "--skip_umi_extract" - description: "Skip umi_tools extract step." - info: null - default: - - false - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean_true" - name: "--skip_qc" - description: "Skip all QC steps except for MultiQC." - info: null - direction: "input" - - type: "boolean_true" - name: "--skip_markduplicates" - description: "Skip picard MarkDuplicates step." - info: null - direction: "input" - - type: "boolean_true" - name: "--skip_stringtie" - description: "Skip StringTie." - info: null - direction: "input" - - type: "boolean_true" - name: "--skip_biotype_qc" - description: "Skip additional featureCounts process for biotype QC." - info: null - direction: "input" - - type: "boolean_true" - name: "--skip_bigwig" - description: "Skip bigWig file creation." - info: null - direction: "input" - - type: "boolean_true" - name: "--skip_preseq" - description: "Skip Preseq." - info: null - direction: "input" - - type: "boolean_true" - name: "--skip_deseq2_qc" - description: "Skip DESeq2 PCA and heatmap plotting." - info: null - direction: "input" - - type: "boolean_true" - name: "skip_dupradar" - description: "Skip dupRadar." - info: null - direction: "input" - - type: "boolean_true" - name: "skip_rseqc" - description: "Skip RSeQC." - info: null - direction: "input" - - type: "boolean_true" - name: "skip_multiqc" - description: "Skip MultiQC." - info: null - direction: "input" -- name: "Other process arguments" - arguments: - - type: "string" - name: "--extra_fq_subsample_args" - description: "Extra arguments to pass to fq subsample command in addition to defaults\ - \ defined by the pipeline." - info: null - default: - - " --record-count 1000000 --seed 1" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--extra_picard_args" - description: "Extra arguments to pass to picard MarkDuplicates command in addition\ - \ to defaults defined by the pipeline." - info: null - default: - - " --ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT\ - \ --TMP_DIR tmp" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--extra_bedtools_args" - description: "Extra arguments to pass to bedtools genomecov command in addition\ - \ to defaults defined by the pipeline." - info: null - default: - - " -split -du" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--extra_featurecounts_args" - description: "Extra arguments to pass to featureCounts command in addition to\ - \ defaults defined by the pipeline" - info: null - default: - - " -B -C" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--extra_preseq_args" - description: "Extra arguments to pass to preseq lc_extrap command in addition\ - \ to defaults defined by the pipeline" - info: null - default: - - "-verbose -seed 1 -seg_len 100000000" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--pca_header_multiqc" - info: null - default: - - "assets/multiqc/deseq2_pca_header.txt" - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--clustering_header_multiqc" - info: null - default: - - "assets/multiqc/deseq2_clustering_header.txt" - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean" - name: "--deseq2_vst" - description: "Use vst transformation instead of rlog with DESeq2" - info: null - default: - - true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--extra_deseq2_args" - info: null - default: - - "--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--extra_deseq2_args2" - info: null - default: - - "star_salmon" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--rseqc_modules" - description: "Specify the RSeQC modules to run_wf" - info: null - default: - - "bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication" - required: false - choices: - - "bam_stat" - - "inner_distance" - - "infer_experiment" - - "junction_annotation" - - "junction_saturation" - - "read_distribution" - - "read_duplication" - - "tin" - direction: "input" - multiple: true - multiple_sep: "," -- name: "Multiqc paramenters" - arguments: - - type: "file" - name: "--multiqc_custom_config" - info: null - default: - - "assets/multiqc_config.yml" - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--multiqc_title" - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--multiqc_methods_description" - info: null - default: - - "assets/methods_description_template.yml" - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" -- name: "Output" - arguments: - - type: "file" - name: "--output_fasta" - info: null - default: - - "genome/reference_genome.fasta" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--output_gtf" - info: null - default: - - "genome/gene_annotation.gtf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--output_transcript_fasta" - info: null - default: - - "genome/transcriptome.fasta" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--output_gene_bed" - info: null - default: - - "genome/gene_annotation.bed" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--output_star_index" - description: "Path to STAR index." - info: null - default: - - "genome/index/STAR" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--output_salmon_index" - description: "Path to Salmon index." - info: null - default: - - "genome/index/Salmon" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--output_bbsplit_index" - description: "Path to BBSplit index." - info: null - default: - - "genome/index/BBSplit" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--output_kallisto_index" - description: "Path to Kallisto index." - info: null - default: - - "genome/index/Kallisto" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--output_fastq_1" - description: "Path to output directory" - info: null - default: - - "fastq/$id.read_1.fastq" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--output_fastq_2" - description: "Path to output directory" - info: null - default: - - "fastq/$id.read_2.fastq" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--fastqc_html_1" - description: "FastQC HTML report for read 1." - info: null - default: - - "fastqc_raw/$id.read_1.fastqc.html" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--fastqc_html_2" - description: "FastQC HTML report for read 2." - info: null - default: - - "fastqc_raw/$id.read_2.fastqc.html" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--fastqc_zip_1" - description: "FastQC report archive for read 1." - info: null - default: - - "fastqc_raw/$id.read_1.fastqc.zip" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--fastqc_zip_2" - description: "FastQC report archive for read 2." - info: null - default: - - "fastqc_raw/$id.read_2.fastqc.zip" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--trim_log_1" - info: null - default: - - "trimgalore/$id.read_1.trimming_report.txt" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--trim_log_2" - info: null - default: - - "trimgalore/$id.read_2.trimming_report.txt" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--trim_html_1" - info: null - default: - - "fastqc_trim/$id.read_1.trimmed_fastqc.html" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--trim_html_2" - info: null - default: - - "fastqc_trim/$id.read_2.trimmed_fastqc.html" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--trim_zip_1" - info: null - default: - - "fastqc_trim/$id.read_1.trimmed_fastqc.zip" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--trim_zip_2" - info: null - default: - - "fastqc_trim/$id.read_2.trimmed_fastqc.zip" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--sortmerna_log" - description: "Sortmerna log file." - info: null - default: - - "sortmerna/$id.log" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--star_alignment" - info: null - default: - - "STAR_alignment/$id" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--genome_bam_sorted" - info: null - default: - - "STAR_alignment/genome_processed/$id.genome.bam" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--genome_bam_index" - info: null - default: - - "STAR_alignment/genome_processed/$id.genome.bam.bai" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--genome_bam_stats" - info: null - default: - - "samtools_stats/$id.genome.stats" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--genome_bam_flagstat" - info: null - default: - - "samtools_stats/$id.genome.flagstat" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--genome_bam_idxstats" - info: null - default: - - "samtools_stats/$id.genome.idxstats" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--transcriptome_bam" - info: null - default: - - "STAR_alignment/transcriptome_processed/$id.transcriptome.bam" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--transcriptome_bam_index" - info: null - default: - - "STAR_alignment/transcriptome_processed/$id.transcriptome.bam.bai" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--transcriptome_bam_stats" - info: null - default: - - "samtools_stats/$id.transcriptome.stats" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--transcriptome_bam_flagstat" - info: null - default: - - "samtools_stats/$id.transcriptome.flagstat" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--transcriptome_bam_idxstats" - info: null - default: - - "samtools_stats/$id.transcriptome.idxstats" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--salmon_quant_results" - info: null - default: - - "salmon/$id" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--tpm_gene" - info: null - default: - - "salmon/gene_tpm.tsv" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--counts_gene" - info: null - default: - - "salmon/gene_counts.tsv" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--counts_gene_length_scaled" - info: null - default: - - "salmon/gene_counts_length_scaled.tsv" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--counts_gene_scaled" - info: null - default: - - "salmon/gene_counts_scaled.tsv" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--tpm_transcript" - info: null - default: - - "salmon/transcript_tpm.tsv" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--counts_transcript" - info: null - default: - - "salmon/transcript_counts.tsv" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--salmon_merged_summarizedexperiment" - info: null - default: - - "salmon/summarizedexperiment" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--markduplicates_metrics" - info: null - default: - - "picard/$id.sorted.MarkDuplicates.metrics.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--stringtie_transcript_gtf" - info: null - default: - - "stringtie/$id.transcripts.gtf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--stringtie_coverage_gtf" - info: null - default: - - "stringtie/$id.coverage.gtf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--stringtie_abundance" - info: null - default: - - "stringtie/$id.gene_abundance.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--stringtie_ballgown" - info: null - default: - - "stringtie/$id.ballgown" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--featurecounts" - info: null - default: - - "featurecounts/$id.featureCounts.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--featurecounts_summary" - info: null - default: - - "featurecounts/$id.featureCounts.txt.summary" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--featurecounts_multiqc" - info: null - default: - - "featurecounts/$id.featureCounts_mqc.tsv" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--featurecounts_rrna_multiqc" - info: null - default: - - "featurecounts/$id.featureCounts_rrna_mqc.tsv" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--bedgraph_forward" - info: null - default: - - "bedgraph/$id.forward.bedgraph" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--bedgraph_reverse" - info: null - default: - - "bedgraph/$id.reverse.bedgraph" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--bigwig_forward" - info: null - default: - - "bigwig/$id.forward.bigwig" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--bigwig_reverse" - info: null - default: - - "bigwig/$id.reverse.bigwig" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--preseq_output" - info: null - default: - - "preseq/$id.lc_extrap.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--bamstat_output" - description: "Path to output file (txt) of mapping quality statistics" - info: null - default: - - "RSeQC/bamstat/$id.mapping_quality.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--strandedness_output" - description: "Path to output report (txt) of inferred strandedness" - info: null - default: - - "RSeQC/inferexperiment/$id.strandedness.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--inner_dist_output_stats" - description: "output file (txt) with summary statistics of inner distances of\ - \ paired reads" - info: null - default: - - "RSeQC/innerdistance/$id.inner_distance.stats" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--inner_dist_output_dist" - description: "output file (txt) with inner distances of all paired reads" - info: null - default: - - "RSeQC/innerdistance/txt/$id.inner_distance.txt" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--inner_dist_output_freq" - description: "output file (txt) with frequencies of inner distances of all paired\ - \ reads" - info: null - default: - - "RSeQC/innerdistance/txt/$id.inner_distance_freq.txt" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--inner_dist_output_plot" - description: "output file (pdf) with histogram plot of of inner distances of all\ - \ paired reads" - info: null - default: - - "RSeQC/innerdistance/pdf/$id.inner_distance_plot.pdf" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--inner_dist_output_plot_r" - description: "output file (R) with script of histogram plot of of inner distances\ - \ of all paired reads" - info: null - default: - - "RSeQC/innerdistance/rscript/$id.inner_distance_plot.r" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--junction_annotation_output_log" - description: "output log of junction annotation script" - info: null - default: - - "RSeQC/junctionannotation/log/$id.junction_annotation.log" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--junction_annotation_output_plot_r" - description: "R script to generate splice_junction and splice_events plot" - info: null - default: - - "RSeQC/junctionannotation/rscript/$id.junction_annotation_plot.r" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--junction_annotation_output_junction_bed" - description: "junction annotation file (bed format)" - info: null - default: - - "RSeQC/junctionannotation/bed/$id.junction_annotation.bed" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--junction_annotation_output_junction_interact" - description: "interact file (bed format) of junctions. Can be uploaded to UCSC\ - \ genome browser or converted to bigInteract (using bedToBigBed program) for\ - \ visualization." - info: null - default: - - "RSeQC/junctionannotation/bed/$id.junction_annotation.Interact.bed" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--junction_annotation_output_junction_sheet" - description: "junction annotation file (xls format)" - info: null - default: - - "RSeQC/junctionannotation/xls/$id.junction_annotation.xls" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--junction_annotation_output_splice_events_plot" - description: "plot of splice events (pdf)" - info: null - default: - - "RSeQC/junctionannotation/pdf/$id.splice_events.pdf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--junction_annotation_output_splice_junctions_plot" - description: "plot of junctions (pdf)" - info: null - default: - - "RSeQC/junctionannotation/pdf/$id.splice_junctions_plot.pdf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--junction_saturation_output_plot_r" - description: "r script to generate junction_saturation_plot plot" - info: null - default: - - "RSeQC/junctionsaturation/rscript/$id.junction_saturation_plot.r" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--junction_saturation_output_plot" - description: "plot of junction saturation (pdf" - info: null - default: - - "RSeQC/junctionsaturation/pdf/$id.junction_saturation_plot.pdf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--read_distribution_output" - description: "output file (txt) of read distribution analysis." - info: null - default: - - "RSeQC/readdistribution/$id.read_distribution.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--read_duplication_output_duplication_rate_plot_r" - description: "R script for generating duplication rate plot" - info: null - default: - - "RSeQC/readduplication/rscrpt/$id.duplication_rate_plot.r" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--read_duplication_output_duplication_rate_plot" - description: "duplication rate plot (pdf)" - info: null - default: - - "RSeQC/readduplication/pdf/$id.duplication_rate_plot.pdf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--read_duplication_output_duplication_rate_mapping" - description: "Summary of mapping-based read duplication" - info: null - default: - - "RSeQC/readduplication/xls/$id.duplication_rate_mapping.xls" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--read_duplication_output_duplication_rate_sequence" - description: "Summary of sequencing-based read duplication" - info: null - default: - - "RSeQC/readduplication/xls/$id.duplication_rate_sequencing.xls" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--tin_output_summary" - description: "summary statistics (txt) of calculated TIN metrics" - info: null - default: - - "RSeQC/tin/txt/$id.tin_summary.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--tin_output_metrics" - description: "file with TIN metrics (xls)" - info: null - default: - - "RSeQC/tin/xls/$id.tin.xls" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--dupradar_output_dupmatrix" - description: "path to output file (txt) of duplicate tag counts" - info: null - default: - - "dupradar/gene_data/$id.dup_matrix.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--dupradar_output_dup_intercept_mqc" - description: "path to output file (txt) of multiqc intercept value DupRadar" - info: null - default: - - "dupradar/mqc_intercept/$id.dup_intercept_mqc.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--dupradar_output_duprate_exp_boxplot" - description: "path to output file (pdf) of distribution of expression box plot" - info: null - default: - - "dupradar/box_plot/$id.duprate_exp_boxplot.pdf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--dupradar_output_duprate_exp_densplot" - description: "path to output file (pdf) of 2D density scatter plot of duplicate\ - \ tag counts" - info: null - default: - - "dupradar/scatter_plot/$id.duprate_exp_densityplot.pdf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--dupradar_output_duprate_exp_denscurve_mqc" - description: "path to output file (pdf) of density curve of gene duplication multiqc" - info: null - default: - - "dupradar/density_curve/$id.duprate_exp_density_curve_mqc.pdf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--dupradar_output_expression_histogram" - description: "path to output file (pdf) of distribution of RPK values per gene\ - \ histogram" - info: null - default: - - "dupradar/histogram/$id.expression_hist.pdf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--dupradar_output_intercept_slope" - info: null - default: - - "dupradar/intercept_slope/$id.intercept_slope.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--qualimap_output_pdf" - info: null - default: - - "qualimap/$id.qualimap_output.pdf" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--qualimap_output_dir" - info: null - default: - - "qualimap/$id" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--deseq2_output" - info: null - default: - - "deseq2_qc" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--multiqc_report" - info: null - default: - - "multiqc/multiqc_report.html" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--multiqc_data" - info: null - default: - - "multiqc/multiqc_data" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--multiqc_plots" - info: null - default: - - "multiqc/multiqc_plots" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--multiqc_versions" - info: null - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--versions" - info: null - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" -resources: -- type: "nextflow_script" - path: "main.nf" - is_executable: true - entrypoint: "run_wf" -description: "A viash workflow for the nf-core/rnaseq pipeline.\n" -info: null -status: "enabled" -requirements: - commands: - - "ps" -dependencies: -- name: "workflows/prepare_genome" - repository: - type: "local" -- name: "cat_fastq" - repository: - type: "local" -- name: "workflows/pre_processing" - repository: - type: "local" -- name: "workflows/genome_alignment_and_quant" - repository: - type: "local" -- name: "workflows/pseudo_alignment_and_quant" - repository: - type: "local" -- name: "workflows/post_processing" - repository: - type: "local" -- name: "workflows/quality_control" - repository: - type: "local" -repositories: -- type: "vsh" - name: "biobox" - repo: "vsh/biobox" - tag: "v0.2.0" -- type: "vsh" - name: "craftbox" - repo: "craftbox" - tag: "v0.1.0" -runners: -- type: "executable" - id: "executable" - docker_setup_strategy: "ifneedbepullelsecachedbuild" -- type: "nextflow" - id: "nextflow" - directives: - tag: "$id" - auto: - simplifyInput: true - simplifyOutput: false - transcript: false - publish: false - config: - labels: - mem1gb: "memory = 1000000000.B" - mem2gb: "memory = 2000000000.B" - mem5gb: "memory = 5000000000.B" - mem10gb: "memory = 10000000000.B" - mem20gb: "memory = 20000000000.B" - mem50gb: "memory = 50000000000.B" - mem100gb: "memory = 100000000000.B" - mem200gb: "memory = 200000000000.B" - mem500gb: "memory = 500000000000.B" - mem1tb: "memory = 1000000000000.B" - mem2tb: "memory = 2000000000000.B" - mem5tb: "memory = 5000000000000.B" - mem10tb: "memory = 10000000000000.B" - mem20tb: "memory = 20000000000000.B" - mem50tb: "memory = 50000000000000.B" - mem100tb: "memory = 100000000000000.B" - mem200tb: "memory = 200000000000000.B" - mem500tb: "memory = 500000000000000.B" - mem1gib: "memory = 1073741824.B" - mem2gib: "memory = 2147483648.B" - mem4gib: "memory = 4294967296.B" - mem8gib: "memory = 8589934592.B" - mem16gib: "memory = 17179869184.B" - mem32gib: "memory = 34359738368.B" - mem64gib: "memory = 68719476736.B" - mem128gib: "memory = 137438953472.B" - mem256gib: "memory = 274877906944.B" - mem512gib: "memory = 549755813888.B" - mem1tib: "memory = 1099511627776.B" - mem2tib: "memory = 2199023255552.B" - mem4tib: "memory = 4398046511104.B" - mem8tib: "memory = 8796093022208.B" - mem16tib: "memory = 17592186044416.B" - mem32tib: "memory = 35184372088832.B" - mem64tib: "memory = 70368744177664.B" - mem128tib: "memory = 140737488355328.B" - mem256tib: "memory = 281474976710656.B" - mem512tib: "memory = 562949953421312.B" - cpu1: "cpus = 1" - cpu2: "cpus = 2" - cpu5: "cpus = 5" - cpu10: "cpus = 10" - cpu20: "cpus = 20" - cpu50: "cpus = 50" - cpu100: "cpus = 100" - cpu200: "cpus = 200" - cpu500: "cpus = 500" - cpu1000: "cpus = 1000" - debug: false - container: "docker" -engines: -- type: "native" - id: "native" -build_info: - config: "src/workflows/rnaseq/config.vsh.yaml" - runner: "executable" - engine: "native" - output: "target/executable/workflows/rnaseq" - executable: "target/executable/workflows/rnaseq/rnaseq" - viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" - dependencies: - - "target/nextflow/workflows/prepare_genome" - - "target/nextflow/cat_fastq" - - "target/nextflow/workflows/pre_processing" - - "target/nextflow/workflows/genome_alignment_and_quant" - - "target/nextflow/workflows/pseudo_alignment_and_quant" - - "target/nextflow/workflows/post_processing" - - "target/nextflow/workflows/quality_control" -package_config: - version: "multiple_fixes" - info: - test_resources: - - path: "gs://viash-hub-test-data/rnaseq/v1" - dest: "testData" - repositories: - - type: "vsh" - name: "biobox" - repo: "vsh/biobox" - tag: "v0.2.0" - - type: "vsh" - name: "craftbox" - repo: "craftbox" - tag: "v0.1.0" - viash_version: "0.9.0" - source: "src" - target: "target" - config_mods: - - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\ - \ := '$id'\n" - - ".engines += { type: \"native\" }" - - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'multiple_fixes'" - organization: "vsh" diff --git a/target/executable/workflows/rnaseq/rnaseq b/target/executable/workflows/rnaseq/rnaseq deleted file mode 100755 index f284027..0000000 --- a/target/executable/workflows/rnaseq/rnaseq +++ /dev/null @@ -1,5075 +0,0 @@ -#!/usr/bin/env bash - -# rnaseq multiple_fixes -# -# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative -# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data -# Intuitive. -# -# The component may contain files which fall under a different license. The -# authors of this component should specify the license in the header of such -# files, or include a separate license file detailing the licenses of all included -# files. - -set -e - -if [ -z "$VIASH_TEMP" ]; then - VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMPDIR} - VIASH_TEMP=${VIASH_TEMP:-$VIASH_TEMPDIR} - VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMP} - VIASH_TEMP=${VIASH_TEMP:-$TMPDIR} - VIASH_TEMP=${VIASH_TEMP:-$TMP} - VIASH_TEMP=${VIASH_TEMP:-$TEMPDIR} - VIASH_TEMP=${VIASH_TEMP:-$TEMP} - VIASH_TEMP=${VIASH_TEMP:-/tmp} -fi - -# define helper functions -# ViashQuote: put quotes around non flag values -# $1 : unquoted string -# return : possibly quoted string -# examples: -# ViashQuote --foo # returns --foo -# ViashQuote bar # returns 'bar' -# Viashquote --foo=bar # returns --foo='bar' -function ViashQuote { - if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then - echo "$1" | sed "s#=\(.*\)#='\1'#" - elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then - echo "$1" - else - echo "'$1'" - fi -} -# ViashRemoveFlags: Remove leading flag -# $1 : string with a possible leading flag -# return : string without possible leading flag -# examples: -# ViashRemoveFlags --foo=bar # returns bar -function ViashRemoveFlags { - echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' -} -# ViashSourceDir: return the path of a bash file, following symlinks -# usage : ViashSourceDir ${BASH_SOURCE[0]} -# $1 : Should always be set to ${BASH_SOURCE[0]} -# returns : The absolute path of the bash file -function ViashSourceDir { - local source="$1" - while [ -h "$source" ]; do - local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )" - source="$(readlink "$source")" - [[ $source != /* ]] && source="$dir/$source" - done - cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd -} -# ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks -# usage : ViashFindTargetDir 'ScriptPath' -# $1 : The location from where to start the upward search -# returns : The absolute path of the '.build.yaml' file -function ViashFindTargetDir { - local source="$1" - while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do - source=${source%/*} - done - echo $source -} -# see https://en.wikipedia.org/wiki/Syslog#Severity_level -VIASH_LOGCODE_EMERGENCY=0 -VIASH_LOGCODE_ALERT=1 -VIASH_LOGCODE_CRITICAL=2 -VIASH_LOGCODE_ERROR=3 -VIASH_LOGCODE_WARNING=4 -VIASH_LOGCODE_NOTICE=5 -VIASH_LOGCODE_INFO=6 -VIASH_LOGCODE_DEBUG=7 -VIASH_VERBOSITY=$VIASH_LOGCODE_NOTICE - -# ViashLog: Log events depending on the verbosity level -# usage: ViashLog 1 alert Oh no something went wrong! -# $1: required verbosity level -# $2: display tag -# $3+: messages to display -# stdout: Your input, prepended by '[$2] '. -function ViashLog { - local required_level="$1" - local display_tag="$2" - shift 2 - if [ $VIASH_VERBOSITY -ge $required_level ]; then - >&2 echo "[$display_tag]" "$@" - fi -} - -# ViashEmergency: log events when the system is unstable -# usage: ViashEmergency Oh no something went wrong. -# stdout: Your input, prepended by '[emergency] '. -function ViashEmergency { - ViashLog $VIASH_LOGCODE_EMERGENCY emergency "$@" -} - -# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) -# usage: ViashAlert Oh no something went wrong. -# stdout: Your input, prepended by '[alert] '. -function ViashAlert { - ViashLog $VIASH_LOGCODE_ALERT alert "$@" -} - -# ViashCritical: log events when a critical condition occurs -# usage: ViashCritical Oh no something went wrong. -# stdout: Your input, prepended by '[critical] '. -function ViashCritical { - ViashLog $VIASH_LOGCODE_CRITICAL critical "$@" -} - -# ViashError: log events when an error condition occurs -# usage: ViashError Oh no something went wrong. -# stdout: Your input, prepended by '[error] '. -function ViashError { - ViashLog $VIASH_LOGCODE_ERROR error "$@" -} - -# ViashWarning: log potentially abnormal events -# usage: ViashWarning Something may have gone wrong. -# stdout: Your input, prepended by '[warning] '. -function ViashWarning { - ViashLog $VIASH_LOGCODE_WARNING warning "$@" -} - -# ViashNotice: log significant but normal events -# usage: ViashNotice This just happened. -# stdout: Your input, prepended by '[notice] '. -function ViashNotice { - ViashLog $VIASH_LOGCODE_NOTICE notice "$@" -} - -# ViashInfo: log normal events -# usage: ViashInfo This just happened. -# stdout: Your input, prepended by '[info] '. -function ViashInfo { - ViashLog $VIASH_LOGCODE_INFO info "$@" -} - -# ViashDebug: log all events, for debugging purposes -# usage: ViashDebug This just happened. -# stdout: Your input, prepended by '[debug] '. -function ViashDebug { - ViashLog $VIASH_LOGCODE_DEBUG debug "$@" -} - -# find source folder of this component -VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` - -# find the root of the built components & dependencies -VIASH_TARGET_DIR=`ViashFindTargetDir $VIASH_META_RESOURCES_DIR` - -# define meta fields -VIASH_META_NAME="rnaseq" -VIASH_META_FUNCTIONALITY_NAME="rnaseq" -VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME" -VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml" -VIASH_META_TEMP_DIR="$VIASH_TEMP" - - -# ViashHelp: Display helpful explanation about this executable -function ViashHelp { - echo "rnaseq multiple_fixes" - echo "" - echo "A viash workflow for the nf-core/rnaseq pipeline." - echo "" - echo "Input:" - echo " --id" - echo " type: string, required parameter" - echo " example: foo" - echo " ID of the sample." - echo "" - echo " --fastq_1" - echo " type: file, required parameter, multiple values allowed, file must exist" - echo " Path to the sample (or read 1 of paired end sample)." - echo "" - echo " --fastq_2" - echo " type: file, multiple values allowed" - echo " Path to read 2 of the sample." - echo "" - echo " --strandedness" - echo " type: string" - echo " default: auto" - echo " choices: [ unstranded, forward, reverse, auto ]" - echo " Sample strand-specificity. Must be one of unstranded, forward, reverse" - echo " or auto" - echo "" - echo "Reference genome options:" - echo " --fasta" - echo " type: file, required parameter, file must exist" - echo " Path to FASTA genome file." - echo "" - echo " --gtf" - echo " type: file, file must exist" - echo " Path to GTF annotation file. This parameter is *mandatory* if --genome" - echo " is not specified." - echo "" - echo " --gff" - echo " type: file, file must exist" - echo " Path to GFF3 annotation file. Required if \"--gtf\" is not specified." - echo "" - echo " --additional_fasta" - echo " type: file, file must exist" - echo " FASTA file to concatenate to genome FASTA file e.g. containing spike-in" - echo " sequences." - echo "" - echo " --transcript_fasta" - echo " type: file, file must exist" - echo " Path to FASTA transcriptome file." - echo "" - echo " --gene_bed" - echo " type: file, file must exist" - echo " Path to BED file containing gene intervals. This will be created from" - echo " the GTF file if not specified." - echo "" - echo " --splicesites" - echo " type: file, file must exist" - echo " Splice sites file required for HISAT2." - echo "" - echo " --star_index" - echo " type: file, file must exist" - echo " Path to directory or tar.gz archive for pre-built STAR index." - echo "" - echo " --rsem_index" - echo " type: file, file must exist" - echo " Path to directory or tar.gz archive for pre-built RSEM index." - echo "" - echo " --salmon_index" - echo " type: file, file must exist" - echo " Path to directory or tar.gz archive for pre-built Salmon index." - echo "" - echo " --kallisto_index" - echo " type: file, file must exist" - echo " Path to directory or tar.gz archive for pre-built Kallisto index." - echo "" - echo " --gencode" - echo " type: boolean_true" - echo " Specify if the GTF annotation is in GENCODE format." - echo "" - echo " --gtf_extra_attributes" - echo " type: string" - echo " default: gene_name" - echo " Additional gene identifiers from the input GTF file when running Salmon." - echo " More than one value can be specified separated by comma." - echo "" - echo " --gtf_group_features" - echo " type: string" - echo " default: gene_id" - echo " Define the attribute type used to group features in the GTF file when" - echo " running Salmon." - echo "" - echo " --featurecounts_group_type" - echo " type: string" - echo " default: gene_biotype" - echo " The attribute type used to group feature types in the GTF file when" - echo " generating the biotype plot with featureCounts." - echo "" - echo " --featurecounts_feature_type" - echo " type: string" - echo " default: exon" - echo " By default, the pipeline assigns reads based on the 'exon' attribute" - echo " within the GTF file." - echo "" - echo "Read trimming options:" - echo " --trimmer" - echo " type: string" - echo " default: trimgalore" - echo " choices: [ trimgalore, fastp ]" - echo " Specify the trimming tool to use." - echo "" - echo " --extra_trimgalore_args" - echo " type: string" - echo " Extra arguments to pass to Trim Galore! command in addition to defaults" - echo " defined by the pipeline." - echo "" - echo " --extra_fastp_args" - echo " type: string" - echo " Extra arguments to pass to fastp command in addition to defaults defined" - echo " by the pipeline." - echo "" - echo " --min_trimmed_reads" - echo " type: integer" - echo " default: 10000" - echo " Minimum number of trimmed reads below which samples are removed from" - echo " further processing. Some downstream steps in the pipeline will fail if" - echo " this threshold is too low." - echo "" - echo "Read filtering options:" - echo " --bbsplit_fasta_list" - echo " type: file, file must exist" - echo " Path to comma-separated file containing a list of reference genomes to" - echo " filter reads against with BBSplit. To use BBSplit, \"--skip_bbsplit\" must" - echo " be explicitly set to \"false\". The file should contain 2 (comma" - echo " separated) columns - short name and full path to reference genome(s)" - echo "" - echo " --bbsplit_index" - echo " type: file, file must exist" - echo " Path to directory or tar.gz archive for pre-built BBSplit index." - echo "" - echo " --remove_ribo_rna" - echo " type: boolean_true" - echo " Enable the removal of reads derived from ribosomal RNA using SortMeRNA." - echo "" - echo " --ribo_database_manifest" - echo " type: file, file must exist" - echo " default: assets/rrna-db-defaults.txt" - echo " Text file containing paths to fasta files (one per line) that will be" - echo " used to create the database for SortMeRNA." - echo "" - echo "UMI options:" - echo " --with_umi" - echo " type: boolean_true" - echo " Enable UMI-based read deduplication." - echo "" - echo " --umitools_extract_method" - echo " type: string" - echo " default: string" - echo " choices: [ string, regex ]" - echo " UMI pattern to use." - echo "" - echo " --umitools_bc_pattern" - echo " type: string" - echo " The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the first 6" - echo " nucleotides of the read are from the UMI." - echo "" - echo " --umitools_bc_pattern2" - echo " type: string" - echo " The UMI barcode pattern to use if the UMI is located in read 2." - echo "" - echo " --umi_discard_read" - echo " type: integer" - echo " default: 0" - echo " choices: [ 0, 1, 2 ]" - echo " After UMI barcode extraction discard either R1 or R2 by setting this" - echo " parameter to 1 or 2, respectively." - echo "" - echo " --umitools_umi_separator" - echo " type: string" - echo " default: _" - echo " The character that separates the UMI in the read name. Most likely a" - echo " colon if you skipped the extraction with UMI-tools and used other" - echo " software." - echo "" - echo " --umitools_grouping_method" - echo " type: string" - echo " default: directional" - echo " choices: [ unique, percentile, cluster, adjacency, directional ]" - echo " Method to use to determine read groups by subsuming those with similar" - echo " UMIs. All methods start by identifying the reads with the same mapping" - echo " position, but treat similar yet nonidentical UMIs differently." - echo "" - echo " --umi_dedup_stats" - echo " type: boolean_true" - echo " Generate output stats when running \"umi_tools dedup\"." - echo "" - echo "Alignment options:" - echo " --aligner" - echo " type: string" - echo " default: star_salmon" - echo " choices: [ star_salmon, star_rsem, hisat2 ]" - echo " Specifies the alignment algorithm to use - available options are" - echo " 'star_salmon', 'star_rsem' and 'hisat2'." - echo "" - echo " --pseudo_aligner" - echo " type: string" - echo " default: salmon" - echo " choices: [ salmon, kallisto ]" - echo " Specifies the pseudo aligner to use - available options are 'salmon'." - echo " Runs in addition to '--aligner'." - echo "" - echo " --pseudo_aligner_kmer_size" - echo " type: integer" - echo " default: 31" - echo " Kmer length passed to indexing step of pseudoaligners." - echo "" - echo " --kallisto_quant_fragment_length" - echo " type: integer" - echo " For single-end mode only, the estimated average fragment length to use" - echo " for quantification with Kallisto." - echo "" - echo " --kallisto_quant_fragment_length_sd" - echo " type: integer" - echo " For single-end mode only, the estimated standard deviation of the" - echo " fragment length for quantification with Kallisto." - echo "" - echo " --bam_csi_index" - echo " type: boolean_true" - echo " Create a CSI index for BAM files instead of the traditional BAI index." - echo " This will be required for genomes with larger chromosome sizes." - echo "" - echo " --salmon_quant_libtype" - echo " type: string" - echo " Override Salmon library type inferred based on strandedness defined in" - echo " meta object." - echo "" - echo " --extra_salmon_quant_args" - echo " type: string" - echo " default: -v" - echo " Extra arguments to pass to salmon quant command in addition to defaults" - echo " defined by the pipeline." - echo "" - echo " --min_mapped_reads" - echo " type: integer" - echo " default: 5" - echo " Minimum percentage of uniquely mapped reads below which samples are" - echo " removed from further processing." - echo "" - echo " --stringtie_ignore_gtf" - echo " type: boolean_true" - echo " Perform reference-guided de novo assembly of transcripts using" - echo " StringTie, i.e. don't restrict to those in GTF file." - echo "" - echo " --extra_stringtie_args" - echo " type: string" - echo " default: -v" - echo " Extra arguments to pass to stringtie command in addition to defaults" - echo " defined by the pipeline." - echo "" - echo " --save_unaligned" - echo " type: boolean_true" - echo " Where possible, save unaligned reads from either STAR, HISAT2 or Salmon" - echo " to the results directory." - echo "" - echo " --save_align_intermeds" - echo " type: boolean_true" - echo " Save the intermediate BAM files from the alignment step." - echo "" - echo " --skip_alignment" - echo " type: boolean_true" - echo " Skip all of the alignment-based processes within the pipeline." - echo "" - echo " --skip_pseudo_alignment" - echo " type: boolean_true" - echo " Skip all of the pseudo-alignment-based processes within the pipeline." - echo "" - echo " --extra_rsem_calculate_expression_args" - echo " type: string" - echo " default: --star --star-output-genome-bam --star-gzipped-read-file" - echo "--estimate-rspd --seed 1" - echo " Extra arguments to pass to rsem-calculate-expression command in addition" - echo " to defaults defined by the pipeline." - echo "" - echo "Process skipping options:" - echo " --skip_fastqc" - echo " type: boolean" - echo " default: false" - echo " Skip FatQC step." - echo "" - echo " --skip_trimming" - echo " type: boolean" - echo " default: false" - echo " Skip the adapter trimming step." - echo "" - echo " --skip_bbsplit" - echo " type: boolean_true" - echo " Skip BBSplit for removal of non-reference genome reads." - echo "" - echo " --skip_umi_extract" - echo " type: boolean" - echo " default: false" - echo " Skip umi_tools extract step." - echo "" - echo " --skip_qc" - echo " type: boolean_true" - echo " Skip all QC steps except for MultiQC." - echo "" - echo " --skip_markduplicates" - echo " type: boolean_true" - echo " Skip picard MarkDuplicates step." - echo "" - echo " --skip_stringtie" - echo " type: boolean_true" - echo " Skip StringTie." - echo "" - echo " --skip_biotype_qc" - echo " type: boolean_true" - echo " Skip additional featureCounts process for biotype QC." - echo "" - echo " --skip_bigwig" - echo " type: boolean_true" - echo " Skip bigWig file creation." - echo "" - echo " --skip_preseq" - echo " type: boolean_true" - echo " Skip Preseq." - echo "" - echo " --skip_deseq2_qc" - echo " type: boolean_true" - echo " Skip DESeq2 PCA and heatmap plotting." - echo "" - echo " skip_dupradar" - echo " type: boolean_true" - echo " Skip dupRadar." - echo "" - echo " skip_rseqc" - echo " type: boolean_true" - echo " Skip RSeQC." - echo "" - echo " skip_multiqc" - echo " type: boolean_true" - echo " Skip MultiQC." - echo "" - echo "Other process arguments:" - echo " --extra_fq_subsample_args" - echo " type: string" - echo " default: --record-count 1000000 --seed 1" - echo " Extra arguments to pass to fq subsample command in addition to defaults" - echo " defined by the pipeline." - echo "" - echo " --extra_picard_args" - echo " type: string" - echo " default: --ASSUME_SORTED true --REMOVE_DUPLICATES false" - echo "--VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp" - echo " Extra arguments to pass to picard MarkDuplicates command in addition to" - echo " defaults defined by the pipeline." - echo "" - echo " --extra_bedtools_args" - echo " type: string" - echo " default: -split -du" - echo " Extra arguments to pass to bedtools genomecov command in addition to" - echo " defaults defined by the pipeline." - echo "" - echo " --extra_featurecounts_args" - echo " type: string" - echo " default: -B -C" - echo " Extra arguments to pass to featureCounts command in addition to defaults" - echo " defined by the pipeline" - echo "" - echo " --extra_preseq_args" - echo " type: string" - echo " default: -verbose -seed 1 -seg_len 100000000" - echo " Extra arguments to pass to preseq lc_extrap command in addition to" - echo " defaults defined by the pipeline" - echo "" - echo " --pca_header_multiqc" - echo " type: file, file must exist" - echo " default: assets/multiqc/deseq2_pca_header.txt" - echo "" - echo " --clustering_header_multiqc" - echo " type: file, file must exist" - echo " default: assets/multiqc/deseq2_clustering_header.txt" - echo "" - echo " --deseq2_vst" - echo " type: boolean" - echo " default: true" - echo " Use vst transformation instead of rlog with DESeq2" - echo "" - echo " --extra_deseq2_args" - echo " type: string" - echo " default: --id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3" - echo "" - echo " --extra_deseq2_args2" - echo " type: string" - echo " default: star_salmon" - echo "" - echo " --rseqc_modules" - echo " type: string, multiple values allowed" - echo " default:" - echo "bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication" - echo " choices: [ bam_stat, inner_distance, infer_experiment," - echo "junction_annotation, junction_saturation, read_distribution, read_duplication," - echo "tin ]" - echo " Specify the RSeQC modules to run_wf" - echo "" - echo "Multiqc paramenters:" - echo " --multiqc_custom_config" - echo " type: file, file must exist" - echo " default: assets/multiqc_config.yml" - echo "" - echo " --multiqc_title" - echo " type: string" - echo "" - echo " --multiqc_methods_description" - echo " type: file, file must exist" - echo " default: assets/methods_description_template.yml" - echo "" - echo "Output:" - echo " --output_fasta" - echo " type: file, output, file must exist" - echo " default: genome/reference_genome.fasta" - echo "" - echo " --output_gtf" - echo " type: file, output, file must exist" - echo " default: genome/gene_annotation.gtf" - echo "" - echo " --output_transcript_fasta" - echo " type: file, output, file must exist" - echo " default: genome/transcriptome.fasta" - echo "" - echo " --output_gene_bed" - echo " type: file, output, file must exist" - echo " default: genome/gene_annotation.bed" - echo "" - echo " --output_star_index" - echo " type: file, output, file must exist" - echo " default: genome/index/STAR" - echo " Path to STAR index." - echo "" - echo " --output_salmon_index" - echo " type: file, output, file must exist" - echo " default: genome/index/Salmon" - echo " Path to Salmon index." - echo "" - echo " --output_bbsplit_index" - echo " type: file, output, file must exist" - echo " default: genome/index/BBSplit" - echo " Path to BBSplit index." - echo "" - echo " --output_kallisto_index" - echo " type: file, output, file must exist" - echo " default: genome/index/Kallisto" - echo " Path to Kallisto index." - echo "" - echo " --output_fastq_1" - echo " type: file, output" - echo " default: fastq/\$id.read_1.fastq" - echo " Path to output directory" - echo "" - echo " --output_fastq_2" - echo " type: file, output" - echo " default: fastq/\$id.read_2.fastq" - echo " Path to output directory" - echo "" - echo " --fastqc_html_1" - echo " type: file, output" - echo " default: fastqc_raw/\$id.read_1.fastqc.html" - echo " FastQC HTML report for read 1." - echo "" - echo " --fastqc_html_2" - echo " type: file, output" - echo " default: fastqc_raw/\$id.read_2.fastqc.html" - echo " FastQC HTML report for read 2." - echo "" - echo " --fastqc_zip_1" - echo " type: file, output" - echo " default: fastqc_raw/\$id.read_1.fastqc.zip" - echo " FastQC report archive for read 1." - echo "" - echo " --fastqc_zip_2" - echo " type: file, output" - echo " default: fastqc_raw/\$id.read_2.fastqc.zip" - echo " FastQC report archive for read 2." - echo "" - echo " --trim_log_1" - echo " type: file, output" - echo " default: trimgalore/\$id.read_1.trimming_report.txt" - echo "" - echo " --trim_log_2" - echo " type: file, output" - echo " default: trimgalore/\$id.read_2.trimming_report.txt" - echo "" - echo " --trim_html_1" - echo " type: file, output" - echo " default: fastqc_trim/\$id.read_1.trimmed_fastqc.html" - echo "" - echo " --trim_html_2" - echo " type: file, output" - echo " default: fastqc_trim/\$id.read_2.trimmed_fastqc.html" - echo "" - echo " --trim_zip_1" - echo " type: file, output" - echo " default: fastqc_trim/\$id.read_1.trimmed_fastqc.zip" - echo "" - echo " --trim_zip_2" - echo " type: file, output" - echo " default: fastqc_trim/\$id.read_2.trimmed_fastqc.zip" - echo "" - echo " --sortmerna_log" - echo " type: file, output" - echo " default: sortmerna/\$id.log" - echo " Sortmerna log file." - echo "" - echo " --star_alignment" - echo " type: file, output, file must exist" - echo " default: STAR_alignment/\$id" - echo "" - echo " --genome_bam_sorted" - echo " type: file, output, file must exist" - echo " default: STAR_alignment/genome_processed/\$id.genome.bam" - echo "" - echo " --genome_bam_index" - echo " type: file, output, file must exist" - echo " default: STAR_alignment/genome_processed/\$id.genome.bam.bai" - echo "" - echo " --genome_bam_stats" - echo " type: file, output, file must exist" - echo " default: samtools_stats/\$id.genome.stats" - echo "" - echo " --genome_bam_flagstat" - echo " type: file, output, file must exist" - echo " default: samtools_stats/\$id.genome.flagstat" - echo "" - echo " --genome_bam_idxstats" - echo " type: file, output, file must exist" - echo " default: samtools_stats/\$id.genome.idxstats" - echo "" - echo " --transcriptome_bam" - echo " type: file, output, file must exist" - echo " default: STAR_alignment/transcriptome_processed/\$id.transcriptome.bam" - echo "" - echo " --transcriptome_bam_index" - echo " type: file, output, file must exist" - echo " default:" - echo "STAR_alignment/transcriptome_processed/\$id.transcriptome.bam.bai" - echo "" - echo " --transcriptome_bam_stats" - echo " type: file, output, file must exist" - echo " default: samtools_stats/\$id.transcriptome.stats" - echo "" - echo " --transcriptome_bam_flagstat" - echo " type: file, output, file must exist" - echo " default: samtools_stats/\$id.transcriptome.flagstat" - echo "" - echo " --transcriptome_bam_idxstats" - echo " type: file, output, file must exist" - echo " default: samtools_stats/\$id.transcriptome.idxstats" - echo "" - echo " --salmon_quant_results" - echo " type: file, output, file must exist" - echo " default: salmon/\$id" - echo "" - echo " --tpm_gene" - echo " type: file, output, file must exist" - echo " default: salmon/gene_tpm.tsv" - echo "" - echo " --counts_gene" - echo " type: file, output, file must exist" - echo " default: salmon/gene_counts.tsv" - echo "" - echo " --counts_gene_length_scaled" - echo " type: file, output, file must exist" - echo " default: salmon/gene_counts_length_scaled.tsv" - echo "" - echo " --counts_gene_scaled" - echo " type: file, output, file must exist" - echo " default: salmon/gene_counts_scaled.tsv" - echo "" - echo " --tpm_transcript" - echo " type: file, output, file must exist" - echo " default: salmon/transcript_tpm.tsv" - echo "" - echo " --counts_transcript" - echo " type: file, output, file must exist" - echo " default: salmon/transcript_counts.tsv" - echo "" - echo " --salmon_merged_summarizedexperiment" - echo " type: file, output, file must exist" - echo " default: salmon/summarizedexperiment" - echo "" - echo " --markduplicates_metrics" - echo " type: file, output, file must exist" - echo " default: picard/\$id.sorted.MarkDuplicates.metrics.txt" - echo "" - echo " --stringtie_transcript_gtf" - echo " type: file, output, file must exist" - echo " default: stringtie/\$id.transcripts.gtf" - echo "" - echo " --stringtie_coverage_gtf" - echo " type: file, output, file must exist" - echo " default: stringtie/\$id.coverage.gtf" - echo "" - echo " --stringtie_abundance" - echo " type: file, output, file must exist" - echo " default: stringtie/\$id.gene_abundance.txt" - echo "" - echo " --stringtie_ballgown" - echo " type: file, output, file must exist" - echo " default: stringtie/\$id.ballgown" - echo "" - echo " --featurecounts" - echo " type: file, output, file must exist" - echo " default: featurecounts/\$id.featureCounts.txt" - echo "" - echo " --featurecounts_summary" - echo " type: file, output, file must exist" - echo " default: featurecounts/\$id.featureCounts.txt.summary" - echo "" - echo " --featurecounts_multiqc" - echo " type: file, output" - echo " default: featurecounts/\$id.featureCounts_mqc.tsv" - echo "" - echo " --featurecounts_rrna_multiqc" - echo " type: file, output" - echo " default: featurecounts/\$id.featureCounts_rrna_mqc.tsv" - echo "" - echo " --bedgraph_forward" - echo " type: file, output, file must exist" - echo " default: bedgraph/\$id.forward.bedgraph" - echo "" - echo " --bedgraph_reverse" - echo " type: file, output, file must exist" - echo " default: bedgraph/\$id.reverse.bedgraph" - echo "" - echo " --bigwig_forward" - echo " type: file, output, file must exist" - echo " default: bigwig/\$id.forward.bigwig" - echo "" - echo " --bigwig_reverse" - echo " type: file, output, file must exist" - echo " default: bigwig/\$id.reverse.bigwig" - echo "" - echo " --preseq_output" - echo " type: file, output, file must exist" - echo " default: preseq/\$id.lc_extrap.txt" - echo "" - echo " --bamstat_output" - echo " type: file, output, file must exist" - echo " default: RSeQC/bamstat/\$id.mapping_quality.txt" - echo " Path to output file (txt) of mapping quality statistics" - echo "" - echo " --strandedness_output" - echo " type: file, output, file must exist" - echo " default: RSeQC/inferexperiment/\$id.strandedness.txt" - echo " Path to output report (txt) of inferred strandedness" - echo "" - echo " --inner_dist_output_stats" - echo " type: file, output" - echo " default: RSeQC/innerdistance/\$id.inner_distance.stats" - echo " output file (txt) with summary statistics of inner distances of paired" - echo " reads" - echo "" - echo " --inner_dist_output_dist" - echo " type: file, output" - echo " default: RSeQC/innerdistance/txt/\$id.inner_distance.txt" - echo " output file (txt) with inner distances of all paired reads" - echo "" - echo " --inner_dist_output_freq" - echo " type: file, output" - echo " default: RSeQC/innerdistance/txt/\$id.inner_distance_freq.txt" - echo " output file (txt) with frequencies of inner distances of all paired" - echo " reads" - echo "" - echo " --inner_dist_output_plot" - echo " type: file, output" - echo " default: RSeQC/innerdistance/pdf/\$id.inner_distance_plot.pdf" - echo " output file (pdf) with histogram plot of of inner distances of all" - echo " paired reads" - echo "" - echo " --inner_dist_output_plot_r" - echo " type: file, output" - echo " default: RSeQC/innerdistance/rscript/\$id.inner_distance_plot.r" - echo " output file (R) with script of histogram plot of of inner distances of" - echo " all paired reads" - echo "" - echo " --junction_annotation_output_log" - echo " type: file, output, file must exist" - echo " default: RSeQC/junctionannotation/log/\$id.junction_annotation.log" - echo " output log of junction annotation script" - echo "" - echo " --junction_annotation_output_plot_r" - echo " type: file, output, file must exist" - echo " default: RSeQC/junctionannotation/rscript/\$id.junction_annotation_plot.r" - echo " R script to generate splice_junction and splice_events plot" - echo "" - echo " --junction_annotation_output_junction_bed" - echo " type: file, output, file must exist" - echo " default: RSeQC/junctionannotation/bed/\$id.junction_annotation.bed" - echo " junction annotation file (bed format)" - echo "" - echo " --junction_annotation_output_junction_interact" - echo " type: file, output, file must exist" - echo " default:" - echo "RSeQC/junctionannotation/bed/\$id.junction_annotation.Interact.bed" - echo " interact file (bed format) of junctions. Can be uploaded to UCSC genome" - echo " browser or converted to bigInteract (using bedToBigBed program) for" - echo " visualization." - echo "" - echo " --junction_annotation_output_junction_sheet" - echo " type: file, output, file must exist" - echo " default: RSeQC/junctionannotation/xls/\$id.junction_annotation.xls" - echo " junction annotation file (xls format)" - echo "" - echo " --junction_annotation_output_splice_events_plot" - echo " type: file, output, file must exist" - echo " default: RSeQC/junctionannotation/pdf/\$id.splice_events.pdf" - echo " plot of splice events (pdf)" - echo "" - echo " --junction_annotation_output_splice_junctions_plot" - echo " type: file, output, file must exist" - echo " default: RSeQC/junctionannotation/pdf/\$id.splice_junctions_plot.pdf" - echo " plot of junctions (pdf)" - echo "" - echo " --junction_saturation_output_plot_r" - echo " type: file, output, file must exist" - echo " default: RSeQC/junctionsaturation/rscript/\$id.junction_saturation_plot.r" - echo " r script to generate junction_saturation_plot plot" - echo "" - echo " --junction_saturation_output_plot" - echo " type: file, output, file must exist" - echo " default: RSeQC/junctionsaturation/pdf/\$id.junction_saturation_plot.pdf" - echo " plot of junction saturation (pdf" - echo "" - echo " --read_distribution_output" - echo " type: file, output, file must exist" - echo " default: RSeQC/readdistribution/\$id.read_distribution.txt" - echo " output file (txt) of read distribution analysis." - echo "" - echo " --read_duplication_output_duplication_rate_plot_r" - echo " type: file, output, file must exist" - echo " default: RSeQC/readduplication/rscrpt/\$id.duplication_rate_plot.r" - echo " R script for generating duplication rate plot" - echo "" - echo " --read_duplication_output_duplication_rate_plot" - echo " type: file, output, file must exist" - echo " default: RSeQC/readduplication/pdf/\$id.duplication_rate_plot.pdf" - echo " duplication rate plot (pdf)" - echo "" - echo " --read_duplication_output_duplication_rate_mapping" - echo " type: file, output, file must exist" - echo " default: RSeQC/readduplication/xls/\$id.duplication_rate_mapping.xls" - echo " Summary of mapping-based read duplication" - echo "" - echo " --read_duplication_output_duplication_rate_sequence" - echo " type: file, output, file must exist" - echo " default: RSeQC/readduplication/xls/\$id.duplication_rate_sequencing.xls" - echo " Summary of sequencing-based read duplication" - echo "" - echo " --tin_output_summary" - echo " type: file, output, file must exist" - echo " default: RSeQC/tin/txt/\$id.tin_summary.txt" - echo " summary statistics (txt) of calculated TIN metrics" - echo "" - echo " --tin_output_metrics" - echo " type: file, output, file must exist" - echo " default: RSeQC/tin/xls/\$id.tin.xls" - echo " file with TIN metrics (xls)" - echo "" - echo " --dupradar_output_dupmatrix" - echo " type: file, output, file must exist" - echo " default: dupradar/gene_data/\$id.dup_matrix.txt" - echo " path to output file (txt) of duplicate tag counts" - echo "" - echo " --dupradar_output_dup_intercept_mqc" - echo " type: file, output, file must exist" - echo " default: dupradar/mqc_intercept/\$id.dup_intercept_mqc.txt" - echo " path to output file (txt) of multiqc intercept value DupRadar" - echo "" - echo " --dupradar_output_duprate_exp_boxplot" - echo " type: file, output, file must exist" - echo " default: dupradar/box_plot/\$id.duprate_exp_boxplot.pdf" - echo " path to output file (pdf) of distribution of expression box plot" - echo "" - echo " --dupradar_output_duprate_exp_densplot" - echo " type: file, output, file must exist" - echo " default: dupradar/scatter_plot/\$id.duprate_exp_densityplot.pdf" - echo " path to output file (pdf) of 2D density scatter plot of duplicate tag" - echo " counts" - echo "" - echo " --dupradar_output_duprate_exp_denscurve_mqc" - echo " type: file, output, file must exist" - echo " default: dupradar/density_curve/\$id.duprate_exp_density_curve_mqc.pdf" - echo " path to output file (pdf) of density curve of gene duplication multiqc" - echo "" - echo " --dupradar_output_expression_histogram" - echo " type: file, output, file must exist" - echo " default: dupradar/histogram/\$id.expression_hist.pdf" - echo " path to output file (pdf) of distribution of RPK values per gene" - echo " histogram" - echo "" - echo " --dupradar_output_intercept_slope" - echo " type: file, output, file must exist" - echo " default: dupradar/intercept_slope/\$id.intercept_slope.txt" - echo "" - echo " --qualimap_output_pdf" - echo " type: file, output" - echo " default: qualimap/\$id.qualimap_output.pdf" - echo "" - echo " --qualimap_output_dir" - echo " type: file, output, file must exist" - echo " default: qualimap/\$id" - echo "" - echo " --deseq2_output" - echo " type: file, output, file must exist" - echo " default: deseq2_qc" - echo "" - echo " --multiqc_report" - echo " type: file, output, file must exist" - echo " default: multiqc/multiqc_report.html" - echo "" - echo " --multiqc_data" - echo " type: file, output, file must exist" - echo " default: multiqc/multiqc_data" - echo "" - echo " --multiqc_plots" - echo " type: file, output, file must exist" - echo " default: multiqc/multiqc_plots" - echo "" - echo " --multiqc_versions" - echo " type: file, output, file must exist" - echo "" - echo " --versions" - echo " type: file, output" -} - -# initialise variables -VIASH_MODE='run' -VIASH_ENGINE_ID='native' - -# initialise array -VIASH_POSITIONAL_ARGS='' - -while [[ $# -gt 0 ]]; do - case "$1" in - -h|--help) - ViashHelp - exit - ;; - ---v|---verbose) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" - shift 1 - ;; - ---verbosity) - VIASH_VERBOSITY="$2" - shift 2 - ;; - ---verbosity=*) - VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" - shift 1 - ;; - --version) - echo "rnaseq multiple_fixes" - exit - ;; - --id) - [ -n "$VIASH_PAR_ID" ] && ViashError Bad arguments for option \'--id\': \'$VIASH_PAR_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_ID="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --id. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --id=*) - [ -n "$VIASH_PAR_ID" ] && ViashError Bad arguments for option \'--id=*\': \'$VIASH_PAR_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_ID=$(ViashRemoveFlags "$1") - shift 1 - ;; - --fastq_1) - if [ -z "$VIASH_PAR_FASTQ_1" ]; then - VIASH_PAR_FASTQ_1="$2" - else - VIASH_PAR_FASTQ_1="$VIASH_PAR_FASTQ_1;""$2" - fi - [ $# -lt 2 ] && ViashError Not enough arguments passed to --fastq_1. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --fastq_1=*) - if [ -z "$VIASH_PAR_FASTQ_1" ]; then - VIASH_PAR_FASTQ_1=$(ViashRemoveFlags "$1") - else - VIASH_PAR_FASTQ_1="$VIASH_PAR_FASTQ_1;"$(ViashRemoveFlags "$1") - fi - shift 1 - ;; - --fastq_2) - if [ -z "$VIASH_PAR_FASTQ_2" ]; then - VIASH_PAR_FASTQ_2="$2" - else - VIASH_PAR_FASTQ_2="$VIASH_PAR_FASTQ_2;""$2" - fi - [ $# -lt 2 ] && ViashError Not enough arguments passed to --fastq_2. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --fastq_2=*) - if [ -z "$VIASH_PAR_FASTQ_2" ]; then - VIASH_PAR_FASTQ_2=$(ViashRemoveFlags "$1") - else - VIASH_PAR_FASTQ_2="$VIASH_PAR_FASTQ_2;"$(ViashRemoveFlags "$1") - fi - shift 1 - ;; - --strandedness) - [ -n "$VIASH_PAR_STRANDEDNESS" ] && ViashError Bad arguments for option \'--strandedness\': \'$VIASH_PAR_STRANDEDNESS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_STRANDEDNESS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --strandedness. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --strandedness=*) - [ -n "$VIASH_PAR_STRANDEDNESS" ] && ViashError Bad arguments for option \'--strandedness=*\': \'$VIASH_PAR_STRANDEDNESS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_STRANDEDNESS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --fasta) - [ -n "$VIASH_PAR_FASTA" ] && ViashError Bad arguments for option \'--fasta\': \'$VIASH_PAR_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FASTA="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --fasta. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --fasta=*) - [ -n "$VIASH_PAR_FASTA" ] && ViashError Bad arguments for option \'--fasta=*\': \'$VIASH_PAR_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FASTA=$(ViashRemoveFlags "$1") - shift 1 - ;; - --gtf) - [ -n "$VIASH_PAR_GTF" ] && ViashError Bad arguments for option \'--gtf\': \'$VIASH_PAR_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GTF="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --gtf. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --gtf=*) - [ -n "$VIASH_PAR_GTF" ] && ViashError Bad arguments for option \'--gtf=*\': \'$VIASH_PAR_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GTF=$(ViashRemoveFlags "$1") - shift 1 - ;; - --gff) - [ -n "$VIASH_PAR_GFF" ] && ViashError Bad arguments for option \'--gff\': \'$VIASH_PAR_GFF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GFF="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --gff. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --gff=*) - [ -n "$VIASH_PAR_GFF" ] && ViashError Bad arguments for option \'--gff=*\': \'$VIASH_PAR_GFF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GFF=$(ViashRemoveFlags "$1") - shift 1 - ;; - --additional_fasta) - [ -n "$VIASH_PAR_ADDITIONAL_FASTA" ] && ViashError Bad arguments for option \'--additional_fasta\': \'$VIASH_PAR_ADDITIONAL_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_ADDITIONAL_FASTA="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --additional_fasta. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --additional_fasta=*) - [ -n "$VIASH_PAR_ADDITIONAL_FASTA" ] && ViashError Bad arguments for option \'--additional_fasta=*\': \'$VIASH_PAR_ADDITIONAL_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_ADDITIONAL_FASTA=$(ViashRemoveFlags "$1") - shift 1 - ;; - --transcript_fasta) - [ -n "$VIASH_PAR_TRANSCRIPT_FASTA" ] && ViashError Bad arguments for option \'--transcript_fasta\': \'$VIASH_PAR_TRANSCRIPT_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRANSCRIPT_FASTA="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --transcript_fasta. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --transcript_fasta=*) - [ -n "$VIASH_PAR_TRANSCRIPT_FASTA" ] && ViashError Bad arguments for option \'--transcript_fasta=*\': \'$VIASH_PAR_TRANSCRIPT_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRANSCRIPT_FASTA=$(ViashRemoveFlags "$1") - shift 1 - ;; - --gene_bed) - [ -n "$VIASH_PAR_GENE_BED" ] && ViashError Bad arguments for option \'--gene_bed\': \'$VIASH_PAR_GENE_BED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GENE_BED="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --gene_bed. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --gene_bed=*) - [ -n "$VIASH_PAR_GENE_BED" ] && ViashError Bad arguments for option \'--gene_bed=*\': \'$VIASH_PAR_GENE_BED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GENE_BED=$(ViashRemoveFlags "$1") - shift 1 - ;; - --splicesites) - [ -n "$VIASH_PAR_SPLICESITES" ] && ViashError Bad arguments for option \'--splicesites\': \'$VIASH_PAR_SPLICESITES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SPLICESITES="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --splicesites. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --splicesites=*) - [ -n "$VIASH_PAR_SPLICESITES" ] && ViashError Bad arguments for option \'--splicesites=*\': \'$VIASH_PAR_SPLICESITES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SPLICESITES=$(ViashRemoveFlags "$1") - shift 1 - ;; - --star_index) - [ -n "$VIASH_PAR_STAR_INDEX" ] && ViashError Bad arguments for option \'--star_index\': \'$VIASH_PAR_STAR_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_STAR_INDEX="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --star_index. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --star_index=*) - [ -n "$VIASH_PAR_STAR_INDEX" ] && ViashError Bad arguments for option \'--star_index=*\': \'$VIASH_PAR_STAR_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_STAR_INDEX=$(ViashRemoveFlags "$1") - shift 1 - ;; - --rsem_index) - [ -n "$VIASH_PAR_RSEM_INDEX" ] && ViashError Bad arguments for option \'--rsem_index\': \'$VIASH_PAR_RSEM_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_RSEM_INDEX="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --rsem_index. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --rsem_index=*) - [ -n "$VIASH_PAR_RSEM_INDEX" ] && ViashError Bad arguments for option \'--rsem_index=*\': \'$VIASH_PAR_RSEM_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_RSEM_INDEX=$(ViashRemoveFlags "$1") - shift 1 - ;; - --salmon_index) - [ -n "$VIASH_PAR_SALMON_INDEX" ] && ViashError Bad arguments for option \'--salmon_index\': \'$VIASH_PAR_SALMON_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SALMON_INDEX="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --salmon_index. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --salmon_index=*) - [ -n "$VIASH_PAR_SALMON_INDEX" ] && ViashError Bad arguments for option \'--salmon_index=*\': \'$VIASH_PAR_SALMON_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SALMON_INDEX=$(ViashRemoveFlags "$1") - shift 1 - ;; - --kallisto_index) - [ -n "$VIASH_PAR_KALLISTO_INDEX" ] && ViashError Bad arguments for option \'--kallisto_index\': \'$VIASH_PAR_KALLISTO_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_KALLISTO_INDEX="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --kallisto_index. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --kallisto_index=*) - [ -n "$VIASH_PAR_KALLISTO_INDEX" ] && ViashError Bad arguments for option \'--kallisto_index=*\': \'$VIASH_PAR_KALLISTO_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_KALLISTO_INDEX=$(ViashRemoveFlags "$1") - shift 1 - ;; - --gencode) - [ -n "$VIASH_PAR_GENCODE" ] && ViashError Bad arguments for option \'--gencode\': \'$VIASH_PAR_GENCODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GENCODE=true - shift 1 - ;; - --gtf_extra_attributes) - [ -n "$VIASH_PAR_GTF_EXTRA_ATTRIBUTES" ] && ViashError Bad arguments for option \'--gtf_extra_attributes\': \'$VIASH_PAR_GTF_EXTRA_ATTRIBUTES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GTF_EXTRA_ATTRIBUTES="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --gtf_extra_attributes. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --gtf_extra_attributes=*) - [ -n "$VIASH_PAR_GTF_EXTRA_ATTRIBUTES" ] && ViashError Bad arguments for option \'--gtf_extra_attributes=*\': \'$VIASH_PAR_GTF_EXTRA_ATTRIBUTES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GTF_EXTRA_ATTRIBUTES=$(ViashRemoveFlags "$1") - shift 1 - ;; - --gtf_group_features) - [ -n "$VIASH_PAR_GTF_GROUP_FEATURES" ] && ViashError Bad arguments for option \'--gtf_group_features\': \'$VIASH_PAR_GTF_GROUP_FEATURES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GTF_GROUP_FEATURES="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --gtf_group_features. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --gtf_group_features=*) - [ -n "$VIASH_PAR_GTF_GROUP_FEATURES" ] && ViashError Bad arguments for option \'--gtf_group_features=*\': \'$VIASH_PAR_GTF_GROUP_FEATURES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GTF_GROUP_FEATURES=$(ViashRemoveFlags "$1") - shift 1 - ;; - --featurecounts_group_type) - [ -n "$VIASH_PAR_FEATURECOUNTS_GROUP_TYPE" ] && ViashError Bad arguments for option \'--featurecounts_group_type\': \'$VIASH_PAR_FEATURECOUNTS_GROUP_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FEATURECOUNTS_GROUP_TYPE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --featurecounts_group_type. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --featurecounts_group_type=*) - [ -n "$VIASH_PAR_FEATURECOUNTS_GROUP_TYPE" ] && ViashError Bad arguments for option \'--featurecounts_group_type=*\': \'$VIASH_PAR_FEATURECOUNTS_GROUP_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FEATURECOUNTS_GROUP_TYPE=$(ViashRemoveFlags "$1") - shift 1 - ;; - --featurecounts_feature_type) - [ -n "$VIASH_PAR_FEATURECOUNTS_FEATURE_TYPE" ] && ViashError Bad arguments for option \'--featurecounts_feature_type\': \'$VIASH_PAR_FEATURECOUNTS_FEATURE_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FEATURECOUNTS_FEATURE_TYPE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --featurecounts_feature_type. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --featurecounts_feature_type=*) - [ -n "$VIASH_PAR_FEATURECOUNTS_FEATURE_TYPE" ] && ViashError Bad arguments for option \'--featurecounts_feature_type=*\': \'$VIASH_PAR_FEATURECOUNTS_FEATURE_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FEATURECOUNTS_FEATURE_TYPE=$(ViashRemoveFlags "$1") - shift 1 - ;; - --trimmer) - [ -n "$VIASH_PAR_TRIMMER" ] && ViashError Bad arguments for option \'--trimmer\': \'$VIASH_PAR_TRIMMER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRIMMER="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --trimmer. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --trimmer=*) - [ -n "$VIASH_PAR_TRIMMER" ] && ViashError Bad arguments for option \'--trimmer=*\': \'$VIASH_PAR_TRIMMER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRIMMER=$(ViashRemoveFlags "$1") - shift 1 - ;; - --extra_trimgalore_args) - [ -n "$VIASH_PAR_EXTRA_TRIMGALORE_ARGS" ] && ViashError Bad arguments for option \'--extra_trimgalore_args\': \'$VIASH_PAR_EXTRA_TRIMGALORE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_TRIMGALORE_ARGS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_trimgalore_args. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --extra_trimgalore_args=*) - [ -n "$VIASH_PAR_EXTRA_TRIMGALORE_ARGS" ] && ViashError Bad arguments for option \'--extra_trimgalore_args=*\': \'$VIASH_PAR_EXTRA_TRIMGALORE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_TRIMGALORE_ARGS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --extra_fastp_args) - [ -n "$VIASH_PAR_EXTRA_FASTP_ARGS" ] && ViashError Bad arguments for option \'--extra_fastp_args\': \'$VIASH_PAR_EXTRA_FASTP_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_FASTP_ARGS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_fastp_args. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --extra_fastp_args=*) - [ -n "$VIASH_PAR_EXTRA_FASTP_ARGS" ] && ViashError Bad arguments for option \'--extra_fastp_args=*\': \'$VIASH_PAR_EXTRA_FASTP_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_FASTP_ARGS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --min_trimmed_reads) - [ -n "$VIASH_PAR_MIN_TRIMMED_READS" ] && ViashError Bad arguments for option \'--min_trimmed_reads\': \'$VIASH_PAR_MIN_TRIMMED_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MIN_TRIMMED_READS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --min_trimmed_reads. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --min_trimmed_reads=*) - [ -n "$VIASH_PAR_MIN_TRIMMED_READS" ] && ViashError Bad arguments for option \'--min_trimmed_reads=*\': \'$VIASH_PAR_MIN_TRIMMED_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MIN_TRIMMED_READS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --bbsplit_fasta_list) - [ -n "$VIASH_PAR_BBSPLIT_FASTA_LIST" ] && ViashError Bad arguments for option \'--bbsplit_fasta_list\': \'$VIASH_PAR_BBSPLIT_FASTA_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_BBSPLIT_FASTA_LIST="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --bbsplit_fasta_list. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --bbsplit_fasta_list=*) - [ -n "$VIASH_PAR_BBSPLIT_FASTA_LIST" ] && ViashError Bad arguments for option \'--bbsplit_fasta_list=*\': \'$VIASH_PAR_BBSPLIT_FASTA_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_BBSPLIT_FASTA_LIST=$(ViashRemoveFlags "$1") - shift 1 - ;; - --bbsplit_index) - [ -n "$VIASH_PAR_BBSPLIT_INDEX" ] && ViashError Bad arguments for option \'--bbsplit_index\': \'$VIASH_PAR_BBSPLIT_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_BBSPLIT_INDEX="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --bbsplit_index. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --bbsplit_index=*) - [ -n "$VIASH_PAR_BBSPLIT_INDEX" ] && ViashError Bad arguments for option \'--bbsplit_index=*\': \'$VIASH_PAR_BBSPLIT_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_BBSPLIT_INDEX=$(ViashRemoveFlags "$1") - shift 1 - ;; - --remove_ribo_rna) - [ -n "$VIASH_PAR_REMOVE_RIBO_RNA" ] && ViashError Bad arguments for option \'--remove_ribo_rna\': \'$VIASH_PAR_REMOVE_RIBO_RNA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_REMOVE_RIBO_RNA=true - shift 1 - ;; - --ribo_database_manifest) - [ -n "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ] && ViashError Bad arguments for option \'--ribo_database_manifest\': \'$VIASH_PAR_RIBO_DATABASE_MANIFEST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_RIBO_DATABASE_MANIFEST="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --ribo_database_manifest. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --ribo_database_manifest=*) - [ -n "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ] && ViashError Bad arguments for option \'--ribo_database_manifest=*\': \'$VIASH_PAR_RIBO_DATABASE_MANIFEST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_RIBO_DATABASE_MANIFEST=$(ViashRemoveFlags "$1") - shift 1 - ;; - --with_umi) - [ -n "$VIASH_PAR_WITH_UMI" ] && ViashError Bad arguments for option \'--with_umi\': \'$VIASH_PAR_WITH_UMI\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_WITH_UMI=true - shift 1 - ;; - --umitools_extract_method) - [ -n "$VIASH_PAR_UMITOOLS_EXTRACT_METHOD" ] && ViashError Bad arguments for option \'--umitools_extract_method\': \'$VIASH_PAR_UMITOOLS_EXTRACT_METHOD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_UMITOOLS_EXTRACT_METHOD="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --umitools_extract_method. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --umitools_extract_method=*) - [ -n "$VIASH_PAR_UMITOOLS_EXTRACT_METHOD" ] && ViashError Bad arguments for option \'--umitools_extract_method=*\': \'$VIASH_PAR_UMITOOLS_EXTRACT_METHOD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_UMITOOLS_EXTRACT_METHOD=$(ViashRemoveFlags "$1") - shift 1 - ;; - --umitools_bc_pattern) - [ -n "$VIASH_PAR_UMITOOLS_BC_PATTERN" ] && ViashError Bad arguments for option \'--umitools_bc_pattern\': \'$VIASH_PAR_UMITOOLS_BC_PATTERN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_UMITOOLS_BC_PATTERN="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --umitools_bc_pattern. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --umitools_bc_pattern=*) - [ -n "$VIASH_PAR_UMITOOLS_BC_PATTERN" ] && ViashError Bad arguments for option \'--umitools_bc_pattern=*\': \'$VIASH_PAR_UMITOOLS_BC_PATTERN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_UMITOOLS_BC_PATTERN=$(ViashRemoveFlags "$1") - shift 1 - ;; - --umitools_bc_pattern2) - [ -n "$VIASH_PAR_UMITOOLS_BC_PATTERN2" ] && ViashError Bad arguments for option \'--umitools_bc_pattern2\': \'$VIASH_PAR_UMITOOLS_BC_PATTERN2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_UMITOOLS_BC_PATTERN2="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --umitools_bc_pattern2. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --umitools_bc_pattern2=*) - [ -n "$VIASH_PAR_UMITOOLS_BC_PATTERN2" ] && ViashError Bad arguments for option \'--umitools_bc_pattern2=*\': \'$VIASH_PAR_UMITOOLS_BC_PATTERN2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_UMITOOLS_BC_PATTERN2=$(ViashRemoveFlags "$1") - shift 1 - ;; - --umi_discard_read) - [ -n "$VIASH_PAR_UMI_DISCARD_READ" ] && ViashError Bad arguments for option \'--umi_discard_read\': \'$VIASH_PAR_UMI_DISCARD_READ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_UMI_DISCARD_READ="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --umi_discard_read. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --umi_discard_read=*) - [ -n "$VIASH_PAR_UMI_DISCARD_READ" ] && ViashError Bad arguments for option \'--umi_discard_read=*\': \'$VIASH_PAR_UMI_DISCARD_READ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_UMI_DISCARD_READ=$(ViashRemoveFlags "$1") - shift 1 - ;; - --umitools_umi_separator) - [ -n "$VIASH_PAR_UMITOOLS_UMI_SEPARATOR" ] && ViashError Bad arguments for option \'--umitools_umi_separator\': \'$VIASH_PAR_UMITOOLS_UMI_SEPARATOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_UMITOOLS_UMI_SEPARATOR="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --umitools_umi_separator. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --umitools_umi_separator=*) - [ -n "$VIASH_PAR_UMITOOLS_UMI_SEPARATOR" ] && ViashError Bad arguments for option \'--umitools_umi_separator=*\': \'$VIASH_PAR_UMITOOLS_UMI_SEPARATOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_UMITOOLS_UMI_SEPARATOR=$(ViashRemoveFlags "$1") - shift 1 - ;; - --umitools_grouping_method) - [ -n "$VIASH_PAR_UMITOOLS_GROUPING_METHOD" ] && ViashError Bad arguments for option \'--umitools_grouping_method\': \'$VIASH_PAR_UMITOOLS_GROUPING_METHOD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_UMITOOLS_GROUPING_METHOD="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --umitools_grouping_method. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --umitools_grouping_method=*) - [ -n "$VIASH_PAR_UMITOOLS_GROUPING_METHOD" ] && ViashError Bad arguments for option \'--umitools_grouping_method=*\': \'$VIASH_PAR_UMITOOLS_GROUPING_METHOD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_UMITOOLS_GROUPING_METHOD=$(ViashRemoveFlags "$1") - shift 1 - ;; - --umi_dedup_stats) - [ -n "$VIASH_PAR_UMI_DEDUP_STATS" ] && ViashError Bad arguments for option \'--umi_dedup_stats\': \'$VIASH_PAR_UMI_DEDUP_STATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_UMI_DEDUP_STATS=true - shift 1 - ;; - --aligner) - [ -n "$VIASH_PAR_ALIGNER" ] && ViashError Bad arguments for option \'--aligner\': \'$VIASH_PAR_ALIGNER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_ALIGNER="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --aligner. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --aligner=*) - [ -n "$VIASH_PAR_ALIGNER" ] && ViashError Bad arguments for option \'--aligner=*\': \'$VIASH_PAR_ALIGNER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_ALIGNER=$(ViashRemoveFlags "$1") - shift 1 - ;; - --pseudo_aligner) - [ -n "$VIASH_PAR_PSEUDO_ALIGNER" ] && ViashError Bad arguments for option \'--pseudo_aligner\': \'$VIASH_PAR_PSEUDO_ALIGNER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_PSEUDO_ALIGNER="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --pseudo_aligner. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --pseudo_aligner=*) - [ -n "$VIASH_PAR_PSEUDO_ALIGNER" ] && ViashError Bad arguments for option \'--pseudo_aligner=*\': \'$VIASH_PAR_PSEUDO_ALIGNER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_PSEUDO_ALIGNER=$(ViashRemoveFlags "$1") - shift 1 - ;; - --pseudo_aligner_kmer_size) - [ -n "$VIASH_PAR_PSEUDO_ALIGNER_KMER_SIZE" ] && ViashError Bad arguments for option \'--pseudo_aligner_kmer_size\': \'$VIASH_PAR_PSEUDO_ALIGNER_KMER_SIZE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_PSEUDO_ALIGNER_KMER_SIZE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --pseudo_aligner_kmer_size. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --pseudo_aligner_kmer_size=*) - [ -n "$VIASH_PAR_PSEUDO_ALIGNER_KMER_SIZE" ] && ViashError Bad arguments for option \'--pseudo_aligner_kmer_size=*\': \'$VIASH_PAR_PSEUDO_ALIGNER_KMER_SIZE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_PSEUDO_ALIGNER_KMER_SIZE=$(ViashRemoveFlags "$1") - shift 1 - ;; - --kallisto_quant_fragment_length) - [ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" ] && ViashError Bad arguments for option \'--kallisto_quant_fragment_length\': \'$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --kallisto_quant_fragment_length. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --kallisto_quant_fragment_length=*) - [ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" ] && ViashError Bad arguments for option \'--kallisto_quant_fragment_length=*\': \'$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH=$(ViashRemoveFlags "$1") - shift 1 - ;; - --kallisto_quant_fragment_length_sd) - [ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" ] && ViashError Bad arguments for option \'--kallisto_quant_fragment_length_sd\': \'$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --kallisto_quant_fragment_length_sd. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --kallisto_quant_fragment_length_sd=*) - [ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" ] && ViashError Bad arguments for option \'--kallisto_quant_fragment_length_sd=*\': \'$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD=$(ViashRemoveFlags "$1") - shift 1 - ;; - --bam_csi_index) - [ -n "$VIASH_PAR_BAM_CSI_INDEX" ] && ViashError Bad arguments for option \'--bam_csi_index\': \'$VIASH_PAR_BAM_CSI_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_BAM_CSI_INDEX=true - shift 1 - ;; - --salmon_quant_libtype) - [ -n "$VIASH_PAR_SALMON_QUANT_LIBTYPE" ] && ViashError Bad arguments for option \'--salmon_quant_libtype\': \'$VIASH_PAR_SALMON_QUANT_LIBTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SALMON_QUANT_LIBTYPE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --salmon_quant_libtype. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --salmon_quant_libtype=*) - [ -n "$VIASH_PAR_SALMON_QUANT_LIBTYPE" ] && ViashError Bad arguments for option \'--salmon_quant_libtype=*\': \'$VIASH_PAR_SALMON_QUANT_LIBTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SALMON_QUANT_LIBTYPE=$(ViashRemoveFlags "$1") - shift 1 - ;; - --extra_salmon_quant_args) - [ -n "$VIASH_PAR_EXTRA_SALMON_QUANT_ARGS" ] && ViashError Bad arguments for option \'--extra_salmon_quant_args\': \'$VIASH_PAR_EXTRA_SALMON_QUANT_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_SALMON_QUANT_ARGS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_salmon_quant_args. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --extra_salmon_quant_args=*) - [ -n "$VIASH_PAR_EXTRA_SALMON_QUANT_ARGS" ] && ViashError Bad arguments for option \'--extra_salmon_quant_args=*\': \'$VIASH_PAR_EXTRA_SALMON_QUANT_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_SALMON_QUANT_ARGS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --min_mapped_reads) - [ -n "$VIASH_PAR_MIN_MAPPED_READS" ] && ViashError Bad arguments for option \'--min_mapped_reads\': \'$VIASH_PAR_MIN_MAPPED_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MIN_MAPPED_READS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --min_mapped_reads. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --min_mapped_reads=*) - [ -n "$VIASH_PAR_MIN_MAPPED_READS" ] && ViashError Bad arguments for option \'--min_mapped_reads=*\': \'$VIASH_PAR_MIN_MAPPED_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MIN_MAPPED_READS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --stringtie_ignore_gtf) - [ -n "$VIASH_PAR_STRINGTIE_IGNORE_GTF" ] && ViashError Bad arguments for option \'--stringtie_ignore_gtf\': \'$VIASH_PAR_STRINGTIE_IGNORE_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_STRINGTIE_IGNORE_GTF=true - shift 1 - ;; - --extra_stringtie_args) - [ -n "$VIASH_PAR_EXTRA_STRINGTIE_ARGS" ] && ViashError Bad arguments for option \'--extra_stringtie_args\': \'$VIASH_PAR_EXTRA_STRINGTIE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_STRINGTIE_ARGS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_stringtie_args. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --extra_stringtie_args=*) - [ -n "$VIASH_PAR_EXTRA_STRINGTIE_ARGS" ] && ViashError Bad arguments for option \'--extra_stringtie_args=*\': \'$VIASH_PAR_EXTRA_STRINGTIE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_STRINGTIE_ARGS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --save_unaligned) - [ -n "$VIASH_PAR_SAVE_UNALIGNED" ] && ViashError Bad arguments for option \'--save_unaligned\': \'$VIASH_PAR_SAVE_UNALIGNED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SAVE_UNALIGNED=true - shift 1 - ;; - --save_align_intermeds) - [ -n "$VIASH_PAR_SAVE_ALIGN_INTERMEDS" ] && ViashError Bad arguments for option \'--save_align_intermeds\': \'$VIASH_PAR_SAVE_ALIGN_INTERMEDS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SAVE_ALIGN_INTERMEDS=true - shift 1 - ;; - --skip_alignment) - [ -n "$VIASH_PAR_SKIP_ALIGNMENT" ] && ViashError Bad arguments for option \'--skip_alignment\': \'$VIASH_PAR_SKIP_ALIGNMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SKIP_ALIGNMENT=true - shift 1 - ;; - --skip_pseudo_alignment) - [ -n "$VIASH_PAR_SKIP_PSEUDO_ALIGNMENT" ] && ViashError Bad arguments for option \'--skip_pseudo_alignment\': \'$VIASH_PAR_SKIP_PSEUDO_ALIGNMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SKIP_PSEUDO_ALIGNMENT=true - shift 1 - ;; - --extra_rsem_calculate_expression_args) - [ -n "$VIASH_PAR_EXTRA_RSEM_CALCULATE_EXPRESSION_ARGS" ] && ViashError Bad arguments for option \'--extra_rsem_calculate_expression_args\': \'$VIASH_PAR_EXTRA_RSEM_CALCULATE_EXPRESSION_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_RSEM_CALCULATE_EXPRESSION_ARGS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_rsem_calculate_expression_args. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --extra_rsem_calculate_expression_args=*) - [ -n "$VIASH_PAR_EXTRA_RSEM_CALCULATE_EXPRESSION_ARGS" ] && ViashError Bad arguments for option \'--extra_rsem_calculate_expression_args=*\': \'$VIASH_PAR_EXTRA_RSEM_CALCULATE_EXPRESSION_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_RSEM_CALCULATE_EXPRESSION_ARGS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --skip_fastqc) - [ -n "$VIASH_PAR_SKIP_FASTQC" ] && ViashError Bad arguments for option \'--skip_fastqc\': \'$VIASH_PAR_SKIP_FASTQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SKIP_FASTQC="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --skip_fastqc. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --skip_fastqc=*) - [ -n "$VIASH_PAR_SKIP_FASTQC" ] && ViashError Bad arguments for option \'--skip_fastqc=*\': \'$VIASH_PAR_SKIP_FASTQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SKIP_FASTQC=$(ViashRemoveFlags "$1") - shift 1 - ;; - --skip_trimming) - [ -n "$VIASH_PAR_SKIP_TRIMMING" ] && ViashError Bad arguments for option \'--skip_trimming\': \'$VIASH_PAR_SKIP_TRIMMING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SKIP_TRIMMING="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --skip_trimming. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --skip_trimming=*) - [ -n "$VIASH_PAR_SKIP_TRIMMING" ] && ViashError Bad arguments for option \'--skip_trimming=*\': \'$VIASH_PAR_SKIP_TRIMMING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SKIP_TRIMMING=$(ViashRemoveFlags "$1") - shift 1 - ;; - --skip_bbsplit) - [ -n "$VIASH_PAR_SKIP_BBSPLIT" ] && ViashError Bad arguments for option \'--skip_bbsplit\': \'$VIASH_PAR_SKIP_BBSPLIT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SKIP_BBSPLIT=true - shift 1 - ;; - --skip_umi_extract) - [ -n "$VIASH_PAR_SKIP_UMI_EXTRACT" ] && ViashError Bad arguments for option \'--skip_umi_extract\': \'$VIASH_PAR_SKIP_UMI_EXTRACT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SKIP_UMI_EXTRACT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --skip_umi_extract. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --skip_umi_extract=*) - [ -n "$VIASH_PAR_SKIP_UMI_EXTRACT" ] && ViashError Bad arguments for option \'--skip_umi_extract=*\': \'$VIASH_PAR_SKIP_UMI_EXTRACT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SKIP_UMI_EXTRACT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --skip_qc) - [ -n "$VIASH_PAR_SKIP_QC" ] && ViashError Bad arguments for option \'--skip_qc\': \'$VIASH_PAR_SKIP_QC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SKIP_QC=true - shift 1 - ;; - --skip_markduplicates) - [ -n "$VIASH_PAR_SKIP_MARKDUPLICATES" ] && ViashError Bad arguments for option \'--skip_markduplicates\': \'$VIASH_PAR_SKIP_MARKDUPLICATES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SKIP_MARKDUPLICATES=true - shift 1 - ;; - --skip_stringtie) - [ -n "$VIASH_PAR_SKIP_STRINGTIE" ] && ViashError Bad arguments for option \'--skip_stringtie\': \'$VIASH_PAR_SKIP_STRINGTIE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SKIP_STRINGTIE=true - shift 1 - ;; - --skip_biotype_qc) - [ -n "$VIASH_PAR_SKIP_BIOTYPE_QC" ] && ViashError Bad arguments for option \'--skip_biotype_qc\': \'$VIASH_PAR_SKIP_BIOTYPE_QC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SKIP_BIOTYPE_QC=true - shift 1 - ;; - --skip_bigwig) - [ -n "$VIASH_PAR_SKIP_BIGWIG" ] && ViashError Bad arguments for option \'--skip_bigwig\': \'$VIASH_PAR_SKIP_BIGWIG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SKIP_BIGWIG=true - shift 1 - ;; - --skip_preseq) - [ -n "$VIASH_PAR_SKIP_PRESEQ" ] && ViashError Bad arguments for option \'--skip_preseq\': \'$VIASH_PAR_SKIP_PRESEQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SKIP_PRESEQ=true - shift 1 - ;; - --skip_deseq2_qc) - [ -n "$VIASH_PAR_SKIP_DESEQ2_QC" ] && ViashError Bad arguments for option \'--skip_deseq2_qc\': \'$VIASH_PAR_SKIP_DESEQ2_QC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SKIP_DESEQ2_QC=true - shift 1 - ;; - --extra_fq_subsample_args) - [ -n "$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS" ] && ViashError Bad arguments for option \'--extra_fq_subsample_args\': \'$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_fq_subsample_args. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --extra_fq_subsample_args=*) - [ -n "$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS" ] && ViashError Bad arguments for option \'--extra_fq_subsample_args=*\': \'$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --extra_picard_args) - [ -n "$VIASH_PAR_EXTRA_PICARD_ARGS" ] && ViashError Bad arguments for option \'--extra_picard_args\': \'$VIASH_PAR_EXTRA_PICARD_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_PICARD_ARGS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_picard_args. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --extra_picard_args=*) - [ -n "$VIASH_PAR_EXTRA_PICARD_ARGS" ] && ViashError Bad arguments for option \'--extra_picard_args=*\': \'$VIASH_PAR_EXTRA_PICARD_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_PICARD_ARGS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --extra_bedtools_args) - [ -n "$VIASH_PAR_EXTRA_BEDTOOLS_ARGS" ] && ViashError Bad arguments for option \'--extra_bedtools_args\': \'$VIASH_PAR_EXTRA_BEDTOOLS_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_BEDTOOLS_ARGS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_bedtools_args. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --extra_bedtools_args=*) - [ -n "$VIASH_PAR_EXTRA_BEDTOOLS_ARGS" ] && ViashError Bad arguments for option \'--extra_bedtools_args=*\': \'$VIASH_PAR_EXTRA_BEDTOOLS_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_BEDTOOLS_ARGS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --extra_featurecounts_args) - [ -n "$VIASH_PAR_EXTRA_FEATURECOUNTS_ARGS" ] && ViashError Bad arguments for option \'--extra_featurecounts_args\': \'$VIASH_PAR_EXTRA_FEATURECOUNTS_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_FEATURECOUNTS_ARGS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_featurecounts_args. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --extra_featurecounts_args=*) - [ -n "$VIASH_PAR_EXTRA_FEATURECOUNTS_ARGS" ] && ViashError Bad arguments for option \'--extra_featurecounts_args=*\': \'$VIASH_PAR_EXTRA_FEATURECOUNTS_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_FEATURECOUNTS_ARGS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --extra_preseq_args) - [ -n "$VIASH_PAR_EXTRA_PRESEQ_ARGS" ] && ViashError Bad arguments for option \'--extra_preseq_args\': \'$VIASH_PAR_EXTRA_PRESEQ_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_PRESEQ_ARGS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_preseq_args. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --extra_preseq_args=*) - [ -n "$VIASH_PAR_EXTRA_PRESEQ_ARGS" ] && ViashError Bad arguments for option \'--extra_preseq_args=*\': \'$VIASH_PAR_EXTRA_PRESEQ_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_PRESEQ_ARGS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --pca_header_multiqc) - [ -n "$VIASH_PAR_PCA_HEADER_MULTIQC" ] && ViashError Bad arguments for option \'--pca_header_multiqc\': \'$VIASH_PAR_PCA_HEADER_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_PCA_HEADER_MULTIQC="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --pca_header_multiqc. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --pca_header_multiqc=*) - [ -n "$VIASH_PAR_PCA_HEADER_MULTIQC" ] && ViashError Bad arguments for option \'--pca_header_multiqc=*\': \'$VIASH_PAR_PCA_HEADER_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_PCA_HEADER_MULTIQC=$(ViashRemoveFlags "$1") - shift 1 - ;; - --clustering_header_multiqc) - [ -n "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ] && ViashError Bad arguments for option \'--clustering_header_multiqc\': \'$VIASH_PAR_CLUSTERING_HEADER_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_CLUSTERING_HEADER_MULTIQC="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --clustering_header_multiqc. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --clustering_header_multiqc=*) - [ -n "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ] && ViashError Bad arguments for option \'--clustering_header_multiqc=*\': \'$VIASH_PAR_CLUSTERING_HEADER_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_CLUSTERING_HEADER_MULTIQC=$(ViashRemoveFlags "$1") - shift 1 - ;; - --deseq2_vst) - [ -n "$VIASH_PAR_DESEQ2_VST" ] && ViashError Bad arguments for option \'--deseq2_vst\': \'$VIASH_PAR_DESEQ2_VST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_DESEQ2_VST="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --deseq2_vst. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --deseq2_vst=*) - [ -n "$VIASH_PAR_DESEQ2_VST" ] && ViashError Bad arguments for option \'--deseq2_vst=*\': \'$VIASH_PAR_DESEQ2_VST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_DESEQ2_VST=$(ViashRemoveFlags "$1") - shift 1 - ;; - --extra_deseq2_args) - [ -n "$VIASH_PAR_EXTRA_DESEQ2_ARGS" ] && ViashError Bad arguments for option \'--extra_deseq2_args\': \'$VIASH_PAR_EXTRA_DESEQ2_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_DESEQ2_ARGS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_deseq2_args. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --extra_deseq2_args=*) - [ -n "$VIASH_PAR_EXTRA_DESEQ2_ARGS" ] && ViashError Bad arguments for option \'--extra_deseq2_args=*\': \'$VIASH_PAR_EXTRA_DESEQ2_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_DESEQ2_ARGS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --extra_deseq2_args2) - [ -n "$VIASH_PAR_EXTRA_DESEQ2_ARGS2" ] && ViashError Bad arguments for option \'--extra_deseq2_args2\': \'$VIASH_PAR_EXTRA_DESEQ2_ARGS2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_DESEQ2_ARGS2="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_deseq2_args2. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --extra_deseq2_args2=*) - [ -n "$VIASH_PAR_EXTRA_DESEQ2_ARGS2" ] && ViashError Bad arguments for option \'--extra_deseq2_args2=*\': \'$VIASH_PAR_EXTRA_DESEQ2_ARGS2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_EXTRA_DESEQ2_ARGS2=$(ViashRemoveFlags "$1") - shift 1 - ;; - --rseqc_modules) - if [ -z "$VIASH_PAR_RSEQC_MODULES" ]; then - VIASH_PAR_RSEQC_MODULES="$2" - else - VIASH_PAR_RSEQC_MODULES="$VIASH_PAR_RSEQC_MODULES,""$2" - fi - [ $# -lt 2 ] && ViashError Not enough arguments passed to --rseqc_modules. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --rseqc_modules=*) - if [ -z "$VIASH_PAR_RSEQC_MODULES" ]; then - VIASH_PAR_RSEQC_MODULES=$(ViashRemoveFlags "$1") - else - VIASH_PAR_RSEQC_MODULES="$VIASH_PAR_RSEQC_MODULES,"$(ViashRemoveFlags "$1") - fi - shift 1 - ;; - --multiqc_custom_config) - [ -n "$VIASH_PAR_MULTIQC_CUSTOM_CONFIG" ] && ViashError Bad arguments for option \'--multiqc_custom_config\': \'$VIASH_PAR_MULTIQC_CUSTOM_CONFIG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MULTIQC_CUSTOM_CONFIG="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --multiqc_custom_config. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --multiqc_custom_config=*) - [ -n "$VIASH_PAR_MULTIQC_CUSTOM_CONFIG" ] && ViashError Bad arguments for option \'--multiqc_custom_config=*\': \'$VIASH_PAR_MULTIQC_CUSTOM_CONFIG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MULTIQC_CUSTOM_CONFIG=$(ViashRemoveFlags "$1") - shift 1 - ;; - --multiqc_title) - [ -n "$VIASH_PAR_MULTIQC_TITLE" ] && ViashError Bad arguments for option \'--multiqc_title\': \'$VIASH_PAR_MULTIQC_TITLE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MULTIQC_TITLE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --multiqc_title. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --multiqc_title=*) - [ -n "$VIASH_PAR_MULTIQC_TITLE" ] && ViashError Bad arguments for option \'--multiqc_title=*\': \'$VIASH_PAR_MULTIQC_TITLE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MULTIQC_TITLE=$(ViashRemoveFlags "$1") - shift 1 - ;; - --multiqc_methods_description) - [ -n "$VIASH_PAR_MULTIQC_METHODS_DESCRIPTION" ] && ViashError Bad arguments for option \'--multiqc_methods_description\': \'$VIASH_PAR_MULTIQC_METHODS_DESCRIPTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MULTIQC_METHODS_DESCRIPTION="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --multiqc_methods_description. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --multiqc_methods_description=*) - [ -n "$VIASH_PAR_MULTIQC_METHODS_DESCRIPTION" ] && ViashError Bad arguments for option \'--multiqc_methods_description=*\': \'$VIASH_PAR_MULTIQC_METHODS_DESCRIPTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MULTIQC_METHODS_DESCRIPTION=$(ViashRemoveFlags "$1") - shift 1 - ;; - --output_fasta) - [ -n "$VIASH_PAR_OUTPUT_FASTA" ] && ViashError Bad arguments for option \'--output_fasta\': \'$VIASH_PAR_OUTPUT_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_FASTA="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_fasta. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --output_fasta=*) - [ -n "$VIASH_PAR_OUTPUT_FASTA" ] && ViashError Bad arguments for option \'--output_fasta=*\': \'$VIASH_PAR_OUTPUT_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_FASTA=$(ViashRemoveFlags "$1") - shift 1 - ;; - --output_gtf) - [ -n "$VIASH_PAR_OUTPUT_GTF" ] && ViashError Bad arguments for option \'--output_gtf\': \'$VIASH_PAR_OUTPUT_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_GTF="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_gtf. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --output_gtf=*) - [ -n "$VIASH_PAR_OUTPUT_GTF" ] && ViashError Bad arguments for option \'--output_gtf=*\': \'$VIASH_PAR_OUTPUT_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_GTF=$(ViashRemoveFlags "$1") - shift 1 - ;; - --output_transcript_fasta) - [ -n "$VIASH_PAR_OUTPUT_TRANSCRIPT_FASTA" ] && ViashError Bad arguments for option \'--output_transcript_fasta\': \'$VIASH_PAR_OUTPUT_TRANSCRIPT_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_TRANSCRIPT_FASTA="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_transcript_fasta. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --output_transcript_fasta=*) - [ -n "$VIASH_PAR_OUTPUT_TRANSCRIPT_FASTA" ] && ViashError Bad arguments for option \'--output_transcript_fasta=*\': \'$VIASH_PAR_OUTPUT_TRANSCRIPT_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_TRANSCRIPT_FASTA=$(ViashRemoveFlags "$1") - shift 1 - ;; - --output_gene_bed) - [ -n "$VIASH_PAR_OUTPUT_GENE_BED" ] && ViashError Bad arguments for option \'--output_gene_bed\': \'$VIASH_PAR_OUTPUT_GENE_BED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_GENE_BED="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_gene_bed. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --output_gene_bed=*) - [ -n "$VIASH_PAR_OUTPUT_GENE_BED" ] && ViashError Bad arguments for option \'--output_gene_bed=*\': \'$VIASH_PAR_OUTPUT_GENE_BED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_GENE_BED=$(ViashRemoveFlags "$1") - shift 1 - ;; - --output_star_index) - [ -n "$VIASH_PAR_OUTPUT_STAR_INDEX" ] && ViashError Bad arguments for option \'--output_star_index\': \'$VIASH_PAR_OUTPUT_STAR_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_STAR_INDEX="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_star_index. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --output_star_index=*) - [ -n "$VIASH_PAR_OUTPUT_STAR_INDEX" ] && ViashError Bad arguments for option \'--output_star_index=*\': \'$VIASH_PAR_OUTPUT_STAR_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_STAR_INDEX=$(ViashRemoveFlags "$1") - shift 1 - ;; - --output_salmon_index) - [ -n "$VIASH_PAR_OUTPUT_SALMON_INDEX" ] && ViashError Bad arguments for option \'--output_salmon_index\': \'$VIASH_PAR_OUTPUT_SALMON_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_SALMON_INDEX="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_salmon_index. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --output_salmon_index=*) - [ -n "$VIASH_PAR_OUTPUT_SALMON_INDEX" ] && ViashError Bad arguments for option \'--output_salmon_index=*\': \'$VIASH_PAR_OUTPUT_SALMON_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_SALMON_INDEX=$(ViashRemoveFlags "$1") - shift 1 - ;; - --output_bbsplit_index) - [ -n "$VIASH_PAR_OUTPUT_BBSPLIT_INDEX" ] && ViashError Bad arguments for option \'--output_bbsplit_index\': \'$VIASH_PAR_OUTPUT_BBSPLIT_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_BBSPLIT_INDEX="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_bbsplit_index. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --output_bbsplit_index=*) - [ -n "$VIASH_PAR_OUTPUT_BBSPLIT_INDEX" ] && ViashError Bad arguments for option \'--output_bbsplit_index=*\': \'$VIASH_PAR_OUTPUT_BBSPLIT_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_BBSPLIT_INDEX=$(ViashRemoveFlags "$1") - shift 1 - ;; - --output_kallisto_index) - [ -n "$VIASH_PAR_OUTPUT_KALLISTO_INDEX" ] && ViashError Bad arguments for option \'--output_kallisto_index\': \'$VIASH_PAR_OUTPUT_KALLISTO_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_KALLISTO_INDEX="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_kallisto_index. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --output_kallisto_index=*) - [ -n "$VIASH_PAR_OUTPUT_KALLISTO_INDEX" ] && ViashError Bad arguments for option \'--output_kallisto_index=*\': \'$VIASH_PAR_OUTPUT_KALLISTO_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_KALLISTO_INDEX=$(ViashRemoveFlags "$1") - shift 1 - ;; - --output_fastq_1) - [ -n "$VIASH_PAR_OUTPUT_FASTQ_1" ] && ViashError Bad arguments for option \'--output_fastq_1\': \'$VIASH_PAR_OUTPUT_FASTQ_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_FASTQ_1="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_fastq_1. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --output_fastq_1=*) - [ -n "$VIASH_PAR_OUTPUT_FASTQ_1" ] && ViashError Bad arguments for option \'--output_fastq_1=*\': \'$VIASH_PAR_OUTPUT_FASTQ_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_FASTQ_1=$(ViashRemoveFlags "$1") - shift 1 - ;; - --output_fastq_2) - [ -n "$VIASH_PAR_OUTPUT_FASTQ_2" ] && ViashError Bad arguments for option \'--output_fastq_2\': \'$VIASH_PAR_OUTPUT_FASTQ_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_FASTQ_2="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_fastq_2. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --output_fastq_2=*) - [ -n "$VIASH_PAR_OUTPUT_FASTQ_2" ] && ViashError Bad arguments for option \'--output_fastq_2=*\': \'$VIASH_PAR_OUTPUT_FASTQ_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_OUTPUT_FASTQ_2=$(ViashRemoveFlags "$1") - shift 1 - ;; - --fastqc_html_1) - [ -n "$VIASH_PAR_FASTQC_HTML_1" ] && ViashError Bad arguments for option \'--fastqc_html_1\': \'$VIASH_PAR_FASTQC_HTML_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FASTQC_HTML_1="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --fastqc_html_1. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --fastqc_html_1=*) - [ -n "$VIASH_PAR_FASTQC_HTML_1" ] && ViashError Bad arguments for option \'--fastqc_html_1=*\': \'$VIASH_PAR_FASTQC_HTML_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FASTQC_HTML_1=$(ViashRemoveFlags "$1") - shift 1 - ;; - --fastqc_html_2) - [ -n "$VIASH_PAR_FASTQC_HTML_2" ] && ViashError Bad arguments for option \'--fastqc_html_2\': \'$VIASH_PAR_FASTQC_HTML_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FASTQC_HTML_2="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --fastqc_html_2. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --fastqc_html_2=*) - [ -n "$VIASH_PAR_FASTQC_HTML_2" ] && ViashError Bad arguments for option \'--fastqc_html_2=*\': \'$VIASH_PAR_FASTQC_HTML_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FASTQC_HTML_2=$(ViashRemoveFlags "$1") - shift 1 - ;; - --fastqc_zip_1) - [ -n "$VIASH_PAR_FASTQC_ZIP_1" ] && ViashError Bad arguments for option \'--fastqc_zip_1\': \'$VIASH_PAR_FASTQC_ZIP_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FASTQC_ZIP_1="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --fastqc_zip_1. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --fastqc_zip_1=*) - [ -n "$VIASH_PAR_FASTQC_ZIP_1" ] && ViashError Bad arguments for option \'--fastqc_zip_1=*\': \'$VIASH_PAR_FASTQC_ZIP_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FASTQC_ZIP_1=$(ViashRemoveFlags "$1") - shift 1 - ;; - --fastqc_zip_2) - [ -n "$VIASH_PAR_FASTQC_ZIP_2" ] && ViashError Bad arguments for option \'--fastqc_zip_2\': \'$VIASH_PAR_FASTQC_ZIP_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FASTQC_ZIP_2="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --fastqc_zip_2. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --fastqc_zip_2=*) - [ -n "$VIASH_PAR_FASTQC_ZIP_2" ] && ViashError Bad arguments for option \'--fastqc_zip_2=*\': \'$VIASH_PAR_FASTQC_ZIP_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FASTQC_ZIP_2=$(ViashRemoveFlags "$1") - shift 1 - ;; - --trim_log_1) - [ -n "$VIASH_PAR_TRIM_LOG_1" ] && ViashError Bad arguments for option \'--trim_log_1\': \'$VIASH_PAR_TRIM_LOG_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRIM_LOG_1="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --trim_log_1. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --trim_log_1=*) - [ -n "$VIASH_PAR_TRIM_LOG_1" ] && ViashError Bad arguments for option \'--trim_log_1=*\': \'$VIASH_PAR_TRIM_LOG_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRIM_LOG_1=$(ViashRemoveFlags "$1") - shift 1 - ;; - --trim_log_2) - [ -n "$VIASH_PAR_TRIM_LOG_2" ] && ViashError Bad arguments for option \'--trim_log_2\': \'$VIASH_PAR_TRIM_LOG_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRIM_LOG_2="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --trim_log_2. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --trim_log_2=*) - [ -n "$VIASH_PAR_TRIM_LOG_2" ] && ViashError Bad arguments for option \'--trim_log_2=*\': \'$VIASH_PAR_TRIM_LOG_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRIM_LOG_2=$(ViashRemoveFlags "$1") - shift 1 - ;; - --trim_html_1) - [ -n "$VIASH_PAR_TRIM_HTML_1" ] && ViashError Bad arguments for option \'--trim_html_1\': \'$VIASH_PAR_TRIM_HTML_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRIM_HTML_1="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --trim_html_1. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --trim_html_1=*) - [ -n "$VIASH_PAR_TRIM_HTML_1" ] && ViashError Bad arguments for option \'--trim_html_1=*\': \'$VIASH_PAR_TRIM_HTML_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRIM_HTML_1=$(ViashRemoveFlags "$1") - shift 1 - ;; - --trim_html_2) - [ -n "$VIASH_PAR_TRIM_HTML_2" ] && ViashError Bad arguments for option \'--trim_html_2\': \'$VIASH_PAR_TRIM_HTML_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRIM_HTML_2="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --trim_html_2. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --trim_html_2=*) - [ -n "$VIASH_PAR_TRIM_HTML_2" ] && ViashError Bad arguments for option \'--trim_html_2=*\': \'$VIASH_PAR_TRIM_HTML_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRIM_HTML_2=$(ViashRemoveFlags "$1") - shift 1 - ;; - --trim_zip_1) - [ -n "$VIASH_PAR_TRIM_ZIP_1" ] && ViashError Bad arguments for option \'--trim_zip_1\': \'$VIASH_PAR_TRIM_ZIP_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRIM_ZIP_1="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --trim_zip_1. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --trim_zip_1=*) - [ -n "$VIASH_PAR_TRIM_ZIP_1" ] && ViashError Bad arguments for option \'--trim_zip_1=*\': \'$VIASH_PAR_TRIM_ZIP_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRIM_ZIP_1=$(ViashRemoveFlags "$1") - shift 1 - ;; - --trim_zip_2) - [ -n "$VIASH_PAR_TRIM_ZIP_2" ] && ViashError Bad arguments for option \'--trim_zip_2\': \'$VIASH_PAR_TRIM_ZIP_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRIM_ZIP_2="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --trim_zip_2. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --trim_zip_2=*) - [ -n "$VIASH_PAR_TRIM_ZIP_2" ] && ViashError Bad arguments for option \'--trim_zip_2=*\': \'$VIASH_PAR_TRIM_ZIP_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRIM_ZIP_2=$(ViashRemoveFlags "$1") - shift 1 - ;; - --sortmerna_log) - [ -n "$VIASH_PAR_SORTMERNA_LOG" ] && ViashError Bad arguments for option \'--sortmerna_log\': \'$VIASH_PAR_SORTMERNA_LOG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SORTMERNA_LOG="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --sortmerna_log. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --sortmerna_log=*) - [ -n "$VIASH_PAR_SORTMERNA_LOG" ] && ViashError Bad arguments for option \'--sortmerna_log=*\': \'$VIASH_PAR_SORTMERNA_LOG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SORTMERNA_LOG=$(ViashRemoveFlags "$1") - shift 1 - ;; - --star_alignment) - [ -n "$VIASH_PAR_STAR_ALIGNMENT" ] && ViashError Bad arguments for option \'--star_alignment\': \'$VIASH_PAR_STAR_ALIGNMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_STAR_ALIGNMENT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --star_alignment. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --star_alignment=*) - [ -n "$VIASH_PAR_STAR_ALIGNMENT" ] && ViashError Bad arguments for option \'--star_alignment=*\': \'$VIASH_PAR_STAR_ALIGNMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_STAR_ALIGNMENT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --genome_bam_sorted) - [ -n "$VIASH_PAR_GENOME_BAM_SORTED" ] && ViashError Bad arguments for option \'--genome_bam_sorted\': \'$VIASH_PAR_GENOME_BAM_SORTED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GENOME_BAM_SORTED="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --genome_bam_sorted. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --genome_bam_sorted=*) - [ -n "$VIASH_PAR_GENOME_BAM_SORTED" ] && ViashError Bad arguments for option \'--genome_bam_sorted=*\': \'$VIASH_PAR_GENOME_BAM_SORTED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GENOME_BAM_SORTED=$(ViashRemoveFlags "$1") - shift 1 - ;; - --genome_bam_index) - [ -n "$VIASH_PAR_GENOME_BAM_INDEX" ] && ViashError Bad arguments for option \'--genome_bam_index\': \'$VIASH_PAR_GENOME_BAM_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GENOME_BAM_INDEX="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --genome_bam_index. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --genome_bam_index=*) - [ -n "$VIASH_PAR_GENOME_BAM_INDEX" ] && ViashError Bad arguments for option \'--genome_bam_index=*\': \'$VIASH_PAR_GENOME_BAM_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GENOME_BAM_INDEX=$(ViashRemoveFlags "$1") - shift 1 - ;; - --genome_bam_stats) - [ -n "$VIASH_PAR_GENOME_BAM_STATS" ] && ViashError Bad arguments for option \'--genome_bam_stats\': \'$VIASH_PAR_GENOME_BAM_STATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GENOME_BAM_STATS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --genome_bam_stats. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --genome_bam_stats=*) - [ -n "$VIASH_PAR_GENOME_BAM_STATS" ] && ViashError Bad arguments for option \'--genome_bam_stats=*\': \'$VIASH_PAR_GENOME_BAM_STATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GENOME_BAM_STATS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --genome_bam_flagstat) - [ -n "$VIASH_PAR_GENOME_BAM_FLAGSTAT" ] && ViashError Bad arguments for option \'--genome_bam_flagstat\': \'$VIASH_PAR_GENOME_BAM_FLAGSTAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GENOME_BAM_FLAGSTAT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --genome_bam_flagstat. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --genome_bam_flagstat=*) - [ -n "$VIASH_PAR_GENOME_BAM_FLAGSTAT" ] && ViashError Bad arguments for option \'--genome_bam_flagstat=*\': \'$VIASH_PAR_GENOME_BAM_FLAGSTAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GENOME_BAM_FLAGSTAT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --genome_bam_idxstats) - [ -n "$VIASH_PAR_GENOME_BAM_IDXSTATS" ] && ViashError Bad arguments for option \'--genome_bam_idxstats\': \'$VIASH_PAR_GENOME_BAM_IDXSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GENOME_BAM_IDXSTATS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --genome_bam_idxstats. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --genome_bam_idxstats=*) - [ -n "$VIASH_PAR_GENOME_BAM_IDXSTATS" ] && ViashError Bad arguments for option \'--genome_bam_idxstats=*\': \'$VIASH_PAR_GENOME_BAM_IDXSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_GENOME_BAM_IDXSTATS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --transcriptome_bam) - [ -n "$VIASH_PAR_TRANSCRIPTOME_BAM" ] && ViashError Bad arguments for option \'--transcriptome_bam\': \'$VIASH_PAR_TRANSCRIPTOME_BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRANSCRIPTOME_BAM="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --transcriptome_bam. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --transcriptome_bam=*) - [ -n "$VIASH_PAR_TRANSCRIPTOME_BAM" ] && ViashError Bad arguments for option \'--transcriptome_bam=*\': \'$VIASH_PAR_TRANSCRIPTOME_BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRANSCRIPTOME_BAM=$(ViashRemoveFlags "$1") - shift 1 - ;; - --transcriptome_bam_index) - [ -n "$VIASH_PAR_TRANSCRIPTOME_BAM_INDEX" ] && ViashError Bad arguments for option \'--transcriptome_bam_index\': \'$VIASH_PAR_TRANSCRIPTOME_BAM_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRANSCRIPTOME_BAM_INDEX="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --transcriptome_bam_index. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --transcriptome_bam_index=*) - [ -n "$VIASH_PAR_TRANSCRIPTOME_BAM_INDEX" ] && ViashError Bad arguments for option \'--transcriptome_bam_index=*\': \'$VIASH_PAR_TRANSCRIPTOME_BAM_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRANSCRIPTOME_BAM_INDEX=$(ViashRemoveFlags "$1") - shift 1 - ;; - --transcriptome_bam_stats) - [ -n "$VIASH_PAR_TRANSCRIPTOME_BAM_STATS" ] && ViashError Bad arguments for option \'--transcriptome_bam_stats\': \'$VIASH_PAR_TRANSCRIPTOME_BAM_STATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRANSCRIPTOME_BAM_STATS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --transcriptome_bam_stats. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --transcriptome_bam_stats=*) - [ -n "$VIASH_PAR_TRANSCRIPTOME_BAM_STATS" ] && ViashError Bad arguments for option \'--transcriptome_bam_stats=*\': \'$VIASH_PAR_TRANSCRIPTOME_BAM_STATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRANSCRIPTOME_BAM_STATS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --transcriptome_bam_flagstat) - [ -n "$VIASH_PAR_TRANSCRIPTOME_BAM_FLAGSTAT" ] && ViashError Bad arguments for option \'--transcriptome_bam_flagstat\': \'$VIASH_PAR_TRANSCRIPTOME_BAM_FLAGSTAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRANSCRIPTOME_BAM_FLAGSTAT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --transcriptome_bam_flagstat. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --transcriptome_bam_flagstat=*) - [ -n "$VIASH_PAR_TRANSCRIPTOME_BAM_FLAGSTAT" ] && ViashError Bad arguments for option \'--transcriptome_bam_flagstat=*\': \'$VIASH_PAR_TRANSCRIPTOME_BAM_FLAGSTAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRANSCRIPTOME_BAM_FLAGSTAT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --transcriptome_bam_idxstats) - [ -n "$VIASH_PAR_TRANSCRIPTOME_BAM_IDXSTATS" ] && ViashError Bad arguments for option \'--transcriptome_bam_idxstats\': \'$VIASH_PAR_TRANSCRIPTOME_BAM_IDXSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRANSCRIPTOME_BAM_IDXSTATS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --transcriptome_bam_idxstats. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --transcriptome_bam_idxstats=*) - [ -n "$VIASH_PAR_TRANSCRIPTOME_BAM_IDXSTATS" ] && ViashError Bad arguments for option \'--transcriptome_bam_idxstats=*\': \'$VIASH_PAR_TRANSCRIPTOME_BAM_IDXSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TRANSCRIPTOME_BAM_IDXSTATS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --salmon_quant_results) - [ -n "$VIASH_PAR_SALMON_QUANT_RESULTS" ] && ViashError Bad arguments for option \'--salmon_quant_results\': \'$VIASH_PAR_SALMON_QUANT_RESULTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SALMON_QUANT_RESULTS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --salmon_quant_results. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --salmon_quant_results=*) - [ -n "$VIASH_PAR_SALMON_QUANT_RESULTS" ] && ViashError Bad arguments for option \'--salmon_quant_results=*\': \'$VIASH_PAR_SALMON_QUANT_RESULTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SALMON_QUANT_RESULTS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --tpm_gene) - [ -n "$VIASH_PAR_TPM_GENE" ] && ViashError Bad arguments for option \'--tpm_gene\': \'$VIASH_PAR_TPM_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TPM_GENE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --tpm_gene. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --tpm_gene=*) - [ -n "$VIASH_PAR_TPM_GENE" ] && ViashError Bad arguments for option \'--tpm_gene=*\': \'$VIASH_PAR_TPM_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TPM_GENE=$(ViashRemoveFlags "$1") - shift 1 - ;; - --counts_gene) - [ -n "$VIASH_PAR_COUNTS_GENE" ] && ViashError Bad arguments for option \'--counts_gene\': \'$VIASH_PAR_COUNTS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_COUNTS_GENE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --counts_gene. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --counts_gene=*) - [ -n "$VIASH_PAR_COUNTS_GENE" ] && ViashError Bad arguments for option \'--counts_gene=*\': \'$VIASH_PAR_COUNTS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_COUNTS_GENE=$(ViashRemoveFlags "$1") - shift 1 - ;; - --counts_gene_length_scaled) - [ -n "$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED" ] && ViashError Bad arguments for option \'--counts_gene_length_scaled\': \'$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_COUNTS_GENE_LENGTH_SCALED="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --counts_gene_length_scaled. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --counts_gene_length_scaled=*) - [ -n "$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED" ] && ViashError Bad arguments for option \'--counts_gene_length_scaled=*\': \'$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_COUNTS_GENE_LENGTH_SCALED=$(ViashRemoveFlags "$1") - shift 1 - ;; - --counts_gene_scaled) - [ -n "$VIASH_PAR_COUNTS_GENE_SCALED" ] && ViashError Bad arguments for option \'--counts_gene_scaled\': \'$VIASH_PAR_COUNTS_GENE_SCALED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_COUNTS_GENE_SCALED="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --counts_gene_scaled. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --counts_gene_scaled=*) - [ -n "$VIASH_PAR_COUNTS_GENE_SCALED" ] && ViashError Bad arguments for option \'--counts_gene_scaled=*\': \'$VIASH_PAR_COUNTS_GENE_SCALED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_COUNTS_GENE_SCALED=$(ViashRemoveFlags "$1") - shift 1 - ;; - --tpm_transcript) - [ -n "$VIASH_PAR_TPM_TRANSCRIPT" ] && ViashError Bad arguments for option \'--tpm_transcript\': \'$VIASH_PAR_TPM_TRANSCRIPT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TPM_TRANSCRIPT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --tpm_transcript. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --tpm_transcript=*) - [ -n "$VIASH_PAR_TPM_TRANSCRIPT" ] && ViashError Bad arguments for option \'--tpm_transcript=*\': \'$VIASH_PAR_TPM_TRANSCRIPT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TPM_TRANSCRIPT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --counts_transcript) - [ -n "$VIASH_PAR_COUNTS_TRANSCRIPT" ] && ViashError Bad arguments for option \'--counts_transcript\': \'$VIASH_PAR_COUNTS_TRANSCRIPT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_COUNTS_TRANSCRIPT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --counts_transcript. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --counts_transcript=*) - [ -n "$VIASH_PAR_COUNTS_TRANSCRIPT" ] && ViashError Bad arguments for option \'--counts_transcript=*\': \'$VIASH_PAR_COUNTS_TRANSCRIPT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_COUNTS_TRANSCRIPT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --salmon_merged_summarizedexperiment) - [ -n "$VIASH_PAR_SALMON_MERGED_SUMMARIZEDEXPERIMENT" ] && ViashError Bad arguments for option \'--salmon_merged_summarizedexperiment\': \'$VIASH_PAR_SALMON_MERGED_SUMMARIZEDEXPERIMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SALMON_MERGED_SUMMARIZEDEXPERIMENT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --salmon_merged_summarizedexperiment. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --salmon_merged_summarizedexperiment=*) - [ -n "$VIASH_PAR_SALMON_MERGED_SUMMARIZEDEXPERIMENT" ] && ViashError Bad arguments for option \'--salmon_merged_summarizedexperiment=*\': \'$VIASH_PAR_SALMON_MERGED_SUMMARIZEDEXPERIMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_SALMON_MERGED_SUMMARIZEDEXPERIMENT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --markduplicates_metrics) - [ -n "$VIASH_PAR_MARKDUPLICATES_METRICS" ] && ViashError Bad arguments for option \'--markduplicates_metrics\': \'$VIASH_PAR_MARKDUPLICATES_METRICS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MARKDUPLICATES_METRICS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --markduplicates_metrics. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --markduplicates_metrics=*) - [ -n "$VIASH_PAR_MARKDUPLICATES_METRICS" ] && ViashError Bad arguments for option \'--markduplicates_metrics=*\': \'$VIASH_PAR_MARKDUPLICATES_METRICS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MARKDUPLICATES_METRICS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --stringtie_transcript_gtf) - [ -n "$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF" ] && ViashError Bad arguments for option \'--stringtie_transcript_gtf\': \'$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --stringtie_transcript_gtf. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --stringtie_transcript_gtf=*) - [ -n "$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF" ] && ViashError Bad arguments for option \'--stringtie_transcript_gtf=*\': \'$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF=$(ViashRemoveFlags "$1") - shift 1 - ;; - --stringtie_coverage_gtf) - [ -n "$VIASH_PAR_STRINGTIE_COVERAGE_GTF" ] && ViashError Bad arguments for option \'--stringtie_coverage_gtf\': \'$VIASH_PAR_STRINGTIE_COVERAGE_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_STRINGTIE_COVERAGE_GTF="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --stringtie_coverage_gtf. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --stringtie_coverage_gtf=*) - [ -n "$VIASH_PAR_STRINGTIE_COVERAGE_GTF" ] && ViashError Bad arguments for option \'--stringtie_coverage_gtf=*\': \'$VIASH_PAR_STRINGTIE_COVERAGE_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_STRINGTIE_COVERAGE_GTF=$(ViashRemoveFlags "$1") - shift 1 - ;; - --stringtie_abundance) - [ -n "$VIASH_PAR_STRINGTIE_ABUNDANCE" ] && ViashError Bad arguments for option \'--stringtie_abundance\': \'$VIASH_PAR_STRINGTIE_ABUNDANCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_STRINGTIE_ABUNDANCE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --stringtie_abundance. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --stringtie_abundance=*) - [ -n "$VIASH_PAR_STRINGTIE_ABUNDANCE" ] && ViashError Bad arguments for option \'--stringtie_abundance=*\': \'$VIASH_PAR_STRINGTIE_ABUNDANCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_STRINGTIE_ABUNDANCE=$(ViashRemoveFlags "$1") - shift 1 - ;; - --stringtie_ballgown) - [ -n "$VIASH_PAR_STRINGTIE_BALLGOWN" ] && ViashError Bad arguments for option \'--stringtie_ballgown\': \'$VIASH_PAR_STRINGTIE_BALLGOWN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_STRINGTIE_BALLGOWN="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --stringtie_ballgown. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --stringtie_ballgown=*) - [ -n "$VIASH_PAR_STRINGTIE_BALLGOWN" ] && ViashError Bad arguments for option \'--stringtie_ballgown=*\': \'$VIASH_PAR_STRINGTIE_BALLGOWN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_STRINGTIE_BALLGOWN=$(ViashRemoveFlags "$1") - shift 1 - ;; - --featurecounts) - [ -n "$VIASH_PAR_FEATURECOUNTS" ] && ViashError Bad arguments for option \'--featurecounts\': \'$VIASH_PAR_FEATURECOUNTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FEATURECOUNTS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --featurecounts. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --featurecounts=*) - [ -n "$VIASH_PAR_FEATURECOUNTS" ] && ViashError Bad arguments for option \'--featurecounts=*\': \'$VIASH_PAR_FEATURECOUNTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FEATURECOUNTS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --featurecounts_summary) - [ -n "$VIASH_PAR_FEATURECOUNTS_SUMMARY" ] && ViashError Bad arguments for option \'--featurecounts_summary\': \'$VIASH_PAR_FEATURECOUNTS_SUMMARY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FEATURECOUNTS_SUMMARY="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --featurecounts_summary. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --featurecounts_summary=*) - [ -n "$VIASH_PAR_FEATURECOUNTS_SUMMARY" ] && ViashError Bad arguments for option \'--featurecounts_summary=*\': \'$VIASH_PAR_FEATURECOUNTS_SUMMARY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FEATURECOUNTS_SUMMARY=$(ViashRemoveFlags "$1") - shift 1 - ;; - --featurecounts_multiqc) - [ -n "$VIASH_PAR_FEATURECOUNTS_MULTIQC" ] && ViashError Bad arguments for option \'--featurecounts_multiqc\': \'$VIASH_PAR_FEATURECOUNTS_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FEATURECOUNTS_MULTIQC="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --featurecounts_multiqc. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --featurecounts_multiqc=*) - [ -n "$VIASH_PAR_FEATURECOUNTS_MULTIQC" ] && ViashError Bad arguments for option \'--featurecounts_multiqc=*\': \'$VIASH_PAR_FEATURECOUNTS_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FEATURECOUNTS_MULTIQC=$(ViashRemoveFlags "$1") - shift 1 - ;; - --featurecounts_rrna_multiqc) - [ -n "$VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC" ] && ViashError Bad arguments for option \'--featurecounts_rrna_multiqc\': \'$VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --featurecounts_rrna_multiqc. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --featurecounts_rrna_multiqc=*) - [ -n "$VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC" ] && ViashError Bad arguments for option \'--featurecounts_rrna_multiqc=*\': \'$VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC=$(ViashRemoveFlags "$1") - shift 1 - ;; - --bedgraph_forward) - [ -n "$VIASH_PAR_BEDGRAPH_FORWARD" ] && ViashError Bad arguments for option \'--bedgraph_forward\': \'$VIASH_PAR_BEDGRAPH_FORWARD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_BEDGRAPH_FORWARD="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --bedgraph_forward. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --bedgraph_forward=*) - [ -n "$VIASH_PAR_BEDGRAPH_FORWARD" ] && ViashError Bad arguments for option \'--bedgraph_forward=*\': \'$VIASH_PAR_BEDGRAPH_FORWARD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_BEDGRAPH_FORWARD=$(ViashRemoveFlags "$1") - shift 1 - ;; - --bedgraph_reverse) - [ -n "$VIASH_PAR_BEDGRAPH_REVERSE" ] && ViashError Bad arguments for option \'--bedgraph_reverse\': \'$VIASH_PAR_BEDGRAPH_REVERSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_BEDGRAPH_REVERSE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --bedgraph_reverse. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --bedgraph_reverse=*) - [ -n "$VIASH_PAR_BEDGRAPH_REVERSE" ] && ViashError Bad arguments for option \'--bedgraph_reverse=*\': \'$VIASH_PAR_BEDGRAPH_REVERSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_BEDGRAPH_REVERSE=$(ViashRemoveFlags "$1") - shift 1 - ;; - --bigwig_forward) - [ -n "$VIASH_PAR_BIGWIG_FORWARD" ] && ViashError Bad arguments for option \'--bigwig_forward\': \'$VIASH_PAR_BIGWIG_FORWARD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_BIGWIG_FORWARD="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --bigwig_forward. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --bigwig_forward=*) - [ -n "$VIASH_PAR_BIGWIG_FORWARD" ] && ViashError Bad arguments for option \'--bigwig_forward=*\': \'$VIASH_PAR_BIGWIG_FORWARD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_BIGWIG_FORWARD=$(ViashRemoveFlags "$1") - shift 1 - ;; - --bigwig_reverse) - [ -n "$VIASH_PAR_BIGWIG_REVERSE" ] && ViashError Bad arguments for option \'--bigwig_reverse\': \'$VIASH_PAR_BIGWIG_REVERSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_BIGWIG_REVERSE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --bigwig_reverse. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --bigwig_reverse=*) - [ -n "$VIASH_PAR_BIGWIG_REVERSE" ] && ViashError Bad arguments for option \'--bigwig_reverse=*\': \'$VIASH_PAR_BIGWIG_REVERSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_BIGWIG_REVERSE=$(ViashRemoveFlags "$1") - shift 1 - ;; - --preseq_output) - [ -n "$VIASH_PAR_PRESEQ_OUTPUT" ] && ViashError Bad arguments for option \'--preseq_output\': \'$VIASH_PAR_PRESEQ_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_PRESEQ_OUTPUT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --preseq_output. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --preseq_output=*) - [ -n "$VIASH_PAR_PRESEQ_OUTPUT" ] && ViashError Bad arguments for option \'--preseq_output=*\': \'$VIASH_PAR_PRESEQ_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_PRESEQ_OUTPUT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --bamstat_output) - [ -n "$VIASH_PAR_BAMSTAT_OUTPUT" ] && ViashError Bad arguments for option \'--bamstat_output\': \'$VIASH_PAR_BAMSTAT_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_BAMSTAT_OUTPUT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --bamstat_output. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --bamstat_output=*) - [ -n "$VIASH_PAR_BAMSTAT_OUTPUT" ] && ViashError Bad arguments for option \'--bamstat_output=*\': \'$VIASH_PAR_BAMSTAT_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_BAMSTAT_OUTPUT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --strandedness_output) - [ -n "$VIASH_PAR_STRANDEDNESS_OUTPUT" ] && ViashError Bad arguments for option \'--strandedness_output\': \'$VIASH_PAR_STRANDEDNESS_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_STRANDEDNESS_OUTPUT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --strandedness_output. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --strandedness_output=*) - [ -n "$VIASH_PAR_STRANDEDNESS_OUTPUT" ] && ViashError Bad arguments for option \'--strandedness_output=*\': \'$VIASH_PAR_STRANDEDNESS_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_STRANDEDNESS_OUTPUT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --inner_dist_output_stats) - [ -n "$VIASH_PAR_INNER_DIST_OUTPUT_STATS" ] && ViashError Bad arguments for option \'--inner_dist_output_stats\': \'$VIASH_PAR_INNER_DIST_OUTPUT_STATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_INNER_DIST_OUTPUT_STATS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --inner_dist_output_stats. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --inner_dist_output_stats=*) - [ -n "$VIASH_PAR_INNER_DIST_OUTPUT_STATS" ] && ViashError Bad arguments for option \'--inner_dist_output_stats=*\': \'$VIASH_PAR_INNER_DIST_OUTPUT_STATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_INNER_DIST_OUTPUT_STATS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --inner_dist_output_dist) - [ -n "$VIASH_PAR_INNER_DIST_OUTPUT_DIST" ] && ViashError Bad arguments for option \'--inner_dist_output_dist\': \'$VIASH_PAR_INNER_DIST_OUTPUT_DIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_INNER_DIST_OUTPUT_DIST="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --inner_dist_output_dist. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --inner_dist_output_dist=*) - [ -n "$VIASH_PAR_INNER_DIST_OUTPUT_DIST" ] && ViashError Bad arguments for option \'--inner_dist_output_dist=*\': \'$VIASH_PAR_INNER_DIST_OUTPUT_DIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_INNER_DIST_OUTPUT_DIST=$(ViashRemoveFlags "$1") - shift 1 - ;; - --inner_dist_output_freq) - [ -n "$VIASH_PAR_INNER_DIST_OUTPUT_FREQ" ] && ViashError Bad arguments for option \'--inner_dist_output_freq\': \'$VIASH_PAR_INNER_DIST_OUTPUT_FREQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_INNER_DIST_OUTPUT_FREQ="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --inner_dist_output_freq. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --inner_dist_output_freq=*) - [ -n "$VIASH_PAR_INNER_DIST_OUTPUT_FREQ" ] && ViashError Bad arguments for option \'--inner_dist_output_freq=*\': \'$VIASH_PAR_INNER_DIST_OUTPUT_FREQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_INNER_DIST_OUTPUT_FREQ=$(ViashRemoveFlags "$1") - shift 1 - ;; - --inner_dist_output_plot) - [ -n "$VIASH_PAR_INNER_DIST_OUTPUT_PLOT" ] && ViashError Bad arguments for option \'--inner_dist_output_plot\': \'$VIASH_PAR_INNER_DIST_OUTPUT_PLOT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_INNER_DIST_OUTPUT_PLOT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --inner_dist_output_plot. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --inner_dist_output_plot=*) - [ -n "$VIASH_PAR_INNER_DIST_OUTPUT_PLOT" ] && ViashError Bad arguments for option \'--inner_dist_output_plot=*\': \'$VIASH_PAR_INNER_DIST_OUTPUT_PLOT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_INNER_DIST_OUTPUT_PLOT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --inner_dist_output_plot_r) - [ -n "$VIASH_PAR_INNER_DIST_OUTPUT_PLOT_R" ] && ViashError Bad arguments for option \'--inner_dist_output_plot_r\': \'$VIASH_PAR_INNER_DIST_OUTPUT_PLOT_R\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_INNER_DIST_OUTPUT_PLOT_R="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --inner_dist_output_plot_r. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --inner_dist_output_plot_r=*) - [ -n "$VIASH_PAR_INNER_DIST_OUTPUT_PLOT_R" ] && ViashError Bad arguments for option \'--inner_dist_output_plot_r=*\': \'$VIASH_PAR_INNER_DIST_OUTPUT_PLOT_R\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_INNER_DIST_OUTPUT_PLOT_R=$(ViashRemoveFlags "$1") - shift 1 - ;; - --junction_annotation_output_log) - [ -n "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_LOG" ] && ViashError Bad arguments for option \'--junction_annotation_output_log\': \'$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_LOG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_LOG="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --junction_annotation_output_log. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --junction_annotation_output_log=*) - [ -n "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_LOG" ] && ViashError Bad arguments for option \'--junction_annotation_output_log=*\': \'$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_LOG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_LOG=$(ViashRemoveFlags "$1") - shift 1 - ;; - --junction_annotation_output_plot_r) - [ -n "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_PLOT_R" ] && ViashError Bad arguments for option \'--junction_annotation_output_plot_r\': \'$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_PLOT_R\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_PLOT_R="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --junction_annotation_output_plot_r. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --junction_annotation_output_plot_r=*) - [ -n "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_PLOT_R" ] && ViashError Bad arguments for option \'--junction_annotation_output_plot_r=*\': \'$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_PLOT_R\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_PLOT_R=$(ViashRemoveFlags "$1") - shift 1 - ;; - --junction_annotation_output_junction_bed) - [ -n "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_BED" ] && ViashError Bad arguments for option \'--junction_annotation_output_junction_bed\': \'$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_BED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_BED="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --junction_annotation_output_junction_bed. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --junction_annotation_output_junction_bed=*) - [ -n "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_BED" ] && ViashError Bad arguments for option \'--junction_annotation_output_junction_bed=*\': \'$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_BED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_BED=$(ViashRemoveFlags "$1") - shift 1 - ;; - --junction_annotation_output_junction_interact) - [ -n "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_INTERACT" ] && ViashError Bad arguments for option \'--junction_annotation_output_junction_interact\': \'$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_INTERACT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_INTERACT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --junction_annotation_output_junction_interact. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --junction_annotation_output_junction_interact=*) - [ -n "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_INTERACT" ] && ViashError Bad arguments for option \'--junction_annotation_output_junction_interact=*\': \'$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_INTERACT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_INTERACT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --junction_annotation_output_junction_sheet) - [ -n "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_SHEET" ] && ViashError Bad arguments for option \'--junction_annotation_output_junction_sheet\': \'$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_SHEET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_SHEET="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --junction_annotation_output_junction_sheet. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --junction_annotation_output_junction_sheet=*) - [ -n "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_SHEET" ] && ViashError Bad arguments for option \'--junction_annotation_output_junction_sheet=*\': \'$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_SHEET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_SHEET=$(ViashRemoveFlags "$1") - shift 1 - ;; - --junction_annotation_output_splice_events_plot) - [ -n "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_EVENTS_PLOT" ] && ViashError Bad arguments for option \'--junction_annotation_output_splice_events_plot\': \'$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_EVENTS_PLOT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_EVENTS_PLOT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --junction_annotation_output_splice_events_plot. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --junction_annotation_output_splice_events_plot=*) - [ -n "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_EVENTS_PLOT" ] && ViashError Bad arguments for option \'--junction_annotation_output_splice_events_plot=*\': \'$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_EVENTS_PLOT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_EVENTS_PLOT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --junction_annotation_output_splice_junctions_plot) - [ -n "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_JUNCTIONS_PLOT" ] && ViashError Bad arguments for option \'--junction_annotation_output_splice_junctions_plot\': \'$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_JUNCTIONS_PLOT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_JUNCTIONS_PLOT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --junction_annotation_output_splice_junctions_plot. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --junction_annotation_output_splice_junctions_plot=*) - [ -n "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_JUNCTIONS_PLOT" ] && ViashError Bad arguments for option \'--junction_annotation_output_splice_junctions_plot=*\': \'$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_JUNCTIONS_PLOT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_JUNCTIONS_PLOT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --junction_saturation_output_plot_r) - [ -n "$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT_R" ] && ViashError Bad arguments for option \'--junction_saturation_output_plot_r\': \'$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT_R\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT_R="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --junction_saturation_output_plot_r. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --junction_saturation_output_plot_r=*) - [ -n "$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT_R" ] && ViashError Bad arguments for option \'--junction_saturation_output_plot_r=*\': \'$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT_R\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT_R=$(ViashRemoveFlags "$1") - shift 1 - ;; - --junction_saturation_output_plot) - [ -n "$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT" ] && ViashError Bad arguments for option \'--junction_saturation_output_plot\': \'$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --junction_saturation_output_plot. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --junction_saturation_output_plot=*) - [ -n "$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT" ] && ViashError Bad arguments for option \'--junction_saturation_output_plot=*\': \'$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --read_distribution_output) - [ -n "$VIASH_PAR_READ_DISTRIBUTION_OUTPUT" ] && ViashError Bad arguments for option \'--read_distribution_output\': \'$VIASH_PAR_READ_DISTRIBUTION_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_READ_DISTRIBUTION_OUTPUT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --read_distribution_output. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --read_distribution_output=*) - [ -n "$VIASH_PAR_READ_DISTRIBUTION_OUTPUT" ] && ViashError Bad arguments for option \'--read_distribution_output=*\': \'$VIASH_PAR_READ_DISTRIBUTION_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_READ_DISTRIBUTION_OUTPUT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --read_duplication_output_duplication_rate_plot_r) - [ -n "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT_R" ] && ViashError Bad arguments for option \'--read_duplication_output_duplication_rate_plot_r\': \'$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT_R\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT_R="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --read_duplication_output_duplication_rate_plot_r. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --read_duplication_output_duplication_rate_plot_r=*) - [ -n "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT_R" ] && ViashError Bad arguments for option \'--read_duplication_output_duplication_rate_plot_r=*\': \'$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT_R\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT_R=$(ViashRemoveFlags "$1") - shift 1 - ;; - --read_duplication_output_duplication_rate_plot) - [ -n "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT" ] && ViashError Bad arguments for option \'--read_duplication_output_duplication_rate_plot\': \'$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --read_duplication_output_duplication_rate_plot. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --read_duplication_output_duplication_rate_plot=*) - [ -n "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT" ] && ViashError Bad arguments for option \'--read_duplication_output_duplication_rate_plot=*\': \'$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --read_duplication_output_duplication_rate_mapping) - [ -n "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_MAPPING" ] && ViashError Bad arguments for option \'--read_duplication_output_duplication_rate_mapping\': \'$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_MAPPING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_MAPPING="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --read_duplication_output_duplication_rate_mapping. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --read_duplication_output_duplication_rate_mapping=*) - [ -n "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_MAPPING" ] && ViashError Bad arguments for option \'--read_duplication_output_duplication_rate_mapping=*\': \'$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_MAPPING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_MAPPING=$(ViashRemoveFlags "$1") - shift 1 - ;; - --read_duplication_output_duplication_rate_sequence) - [ -n "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_SEQUENCE" ] && ViashError Bad arguments for option \'--read_duplication_output_duplication_rate_sequence\': \'$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_SEQUENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_SEQUENCE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --read_duplication_output_duplication_rate_sequence. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --read_duplication_output_duplication_rate_sequence=*) - [ -n "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_SEQUENCE" ] && ViashError Bad arguments for option \'--read_duplication_output_duplication_rate_sequence=*\': \'$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_SEQUENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_SEQUENCE=$(ViashRemoveFlags "$1") - shift 1 - ;; - --tin_output_summary) - [ -n "$VIASH_PAR_TIN_OUTPUT_SUMMARY" ] && ViashError Bad arguments for option \'--tin_output_summary\': \'$VIASH_PAR_TIN_OUTPUT_SUMMARY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TIN_OUTPUT_SUMMARY="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --tin_output_summary. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --tin_output_summary=*) - [ -n "$VIASH_PAR_TIN_OUTPUT_SUMMARY" ] && ViashError Bad arguments for option \'--tin_output_summary=*\': \'$VIASH_PAR_TIN_OUTPUT_SUMMARY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TIN_OUTPUT_SUMMARY=$(ViashRemoveFlags "$1") - shift 1 - ;; - --tin_output_metrics) - [ -n "$VIASH_PAR_TIN_OUTPUT_METRICS" ] && ViashError Bad arguments for option \'--tin_output_metrics\': \'$VIASH_PAR_TIN_OUTPUT_METRICS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TIN_OUTPUT_METRICS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --tin_output_metrics. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --tin_output_metrics=*) - [ -n "$VIASH_PAR_TIN_OUTPUT_METRICS" ] && ViashError Bad arguments for option \'--tin_output_metrics=*\': \'$VIASH_PAR_TIN_OUTPUT_METRICS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_TIN_OUTPUT_METRICS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --dupradar_output_dupmatrix) - [ -n "$VIASH_PAR_DUPRADAR_OUTPUT_DUPMATRIX" ] && ViashError Bad arguments for option \'--dupradar_output_dupmatrix\': \'$VIASH_PAR_DUPRADAR_OUTPUT_DUPMATRIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_DUPRADAR_OUTPUT_DUPMATRIX="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --dupradar_output_dupmatrix. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --dupradar_output_dupmatrix=*) - [ -n "$VIASH_PAR_DUPRADAR_OUTPUT_DUPMATRIX" ] && ViashError Bad arguments for option \'--dupradar_output_dupmatrix=*\': \'$VIASH_PAR_DUPRADAR_OUTPUT_DUPMATRIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_DUPRADAR_OUTPUT_DUPMATRIX=$(ViashRemoveFlags "$1") - shift 1 - ;; - --dupradar_output_dup_intercept_mqc) - [ -n "$VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC" ] && ViashError Bad arguments for option \'--dupradar_output_dup_intercept_mqc\': \'$VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --dupradar_output_dup_intercept_mqc. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --dupradar_output_dup_intercept_mqc=*) - [ -n "$VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC" ] && ViashError Bad arguments for option \'--dupradar_output_dup_intercept_mqc=*\': \'$VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC=$(ViashRemoveFlags "$1") - shift 1 - ;; - --dupradar_output_duprate_exp_boxplot) - [ -n "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_BOXPLOT" ] && ViashError Bad arguments for option \'--dupradar_output_duprate_exp_boxplot\': \'$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_BOXPLOT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_BOXPLOT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --dupradar_output_duprate_exp_boxplot. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --dupradar_output_duprate_exp_boxplot=*) - [ -n "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_BOXPLOT" ] && ViashError Bad arguments for option \'--dupradar_output_duprate_exp_boxplot=*\': \'$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_BOXPLOT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_BOXPLOT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --dupradar_output_duprate_exp_densplot) - [ -n "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSPLOT" ] && ViashError Bad arguments for option \'--dupradar_output_duprate_exp_densplot\': \'$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSPLOT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSPLOT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --dupradar_output_duprate_exp_densplot. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --dupradar_output_duprate_exp_densplot=*) - [ -n "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSPLOT" ] && ViashError Bad arguments for option \'--dupradar_output_duprate_exp_densplot=*\': \'$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSPLOT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSPLOT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --dupradar_output_duprate_exp_denscurve_mqc) - [ -n "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC" ] && ViashError Bad arguments for option \'--dupradar_output_duprate_exp_denscurve_mqc\': \'$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --dupradar_output_duprate_exp_denscurve_mqc. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --dupradar_output_duprate_exp_denscurve_mqc=*) - [ -n "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC" ] && ViashError Bad arguments for option \'--dupradar_output_duprate_exp_denscurve_mqc=*\': \'$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC=$(ViashRemoveFlags "$1") - shift 1 - ;; - --dupradar_output_expression_histogram) - [ -n "$VIASH_PAR_DUPRADAR_OUTPUT_EXPRESSION_HISTOGRAM" ] && ViashError Bad arguments for option \'--dupradar_output_expression_histogram\': \'$VIASH_PAR_DUPRADAR_OUTPUT_EXPRESSION_HISTOGRAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_DUPRADAR_OUTPUT_EXPRESSION_HISTOGRAM="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --dupradar_output_expression_histogram. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --dupradar_output_expression_histogram=*) - [ -n "$VIASH_PAR_DUPRADAR_OUTPUT_EXPRESSION_HISTOGRAM" ] && ViashError Bad arguments for option \'--dupradar_output_expression_histogram=*\': \'$VIASH_PAR_DUPRADAR_OUTPUT_EXPRESSION_HISTOGRAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_DUPRADAR_OUTPUT_EXPRESSION_HISTOGRAM=$(ViashRemoveFlags "$1") - shift 1 - ;; - --dupradar_output_intercept_slope) - [ -n "$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE" ] && ViashError Bad arguments for option \'--dupradar_output_intercept_slope\': \'$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --dupradar_output_intercept_slope. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --dupradar_output_intercept_slope=*) - [ -n "$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE" ] && ViashError Bad arguments for option \'--dupradar_output_intercept_slope=*\': \'$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE=$(ViashRemoveFlags "$1") - shift 1 - ;; - --qualimap_output_pdf) - [ -n "$VIASH_PAR_QUALIMAP_OUTPUT_PDF" ] && ViashError Bad arguments for option \'--qualimap_output_pdf\': \'$VIASH_PAR_QUALIMAP_OUTPUT_PDF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_QUALIMAP_OUTPUT_PDF="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --qualimap_output_pdf. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --qualimap_output_pdf=*) - [ -n "$VIASH_PAR_QUALIMAP_OUTPUT_PDF" ] && ViashError Bad arguments for option \'--qualimap_output_pdf=*\': \'$VIASH_PAR_QUALIMAP_OUTPUT_PDF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_QUALIMAP_OUTPUT_PDF=$(ViashRemoveFlags "$1") - shift 1 - ;; - --qualimap_output_dir) - [ -n "$VIASH_PAR_QUALIMAP_OUTPUT_DIR" ] && ViashError Bad arguments for option \'--qualimap_output_dir\': \'$VIASH_PAR_QUALIMAP_OUTPUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_QUALIMAP_OUTPUT_DIR="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --qualimap_output_dir. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --qualimap_output_dir=*) - [ -n "$VIASH_PAR_QUALIMAP_OUTPUT_DIR" ] && ViashError Bad arguments for option \'--qualimap_output_dir=*\': \'$VIASH_PAR_QUALIMAP_OUTPUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_QUALIMAP_OUTPUT_DIR=$(ViashRemoveFlags "$1") - shift 1 - ;; - --deseq2_output) - [ -n "$VIASH_PAR_DESEQ2_OUTPUT" ] && ViashError Bad arguments for option \'--deseq2_output\': \'$VIASH_PAR_DESEQ2_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_DESEQ2_OUTPUT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --deseq2_output. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --deseq2_output=*) - [ -n "$VIASH_PAR_DESEQ2_OUTPUT" ] && ViashError Bad arguments for option \'--deseq2_output=*\': \'$VIASH_PAR_DESEQ2_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_DESEQ2_OUTPUT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --multiqc_report) - [ -n "$VIASH_PAR_MULTIQC_REPORT" ] && ViashError Bad arguments for option \'--multiqc_report\': \'$VIASH_PAR_MULTIQC_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MULTIQC_REPORT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --multiqc_report. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --multiqc_report=*) - [ -n "$VIASH_PAR_MULTIQC_REPORT" ] && ViashError Bad arguments for option \'--multiqc_report=*\': \'$VIASH_PAR_MULTIQC_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MULTIQC_REPORT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --multiqc_data) - [ -n "$VIASH_PAR_MULTIQC_DATA" ] && ViashError Bad arguments for option \'--multiqc_data\': \'$VIASH_PAR_MULTIQC_DATA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MULTIQC_DATA="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --multiqc_data. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --multiqc_data=*) - [ -n "$VIASH_PAR_MULTIQC_DATA" ] && ViashError Bad arguments for option \'--multiqc_data=*\': \'$VIASH_PAR_MULTIQC_DATA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MULTIQC_DATA=$(ViashRemoveFlags "$1") - shift 1 - ;; - --multiqc_plots) - [ -n "$VIASH_PAR_MULTIQC_PLOTS" ] && ViashError Bad arguments for option \'--multiqc_plots\': \'$VIASH_PAR_MULTIQC_PLOTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MULTIQC_PLOTS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --multiqc_plots. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --multiqc_plots=*) - [ -n "$VIASH_PAR_MULTIQC_PLOTS" ] && ViashError Bad arguments for option \'--multiqc_plots=*\': \'$VIASH_PAR_MULTIQC_PLOTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MULTIQC_PLOTS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --multiqc_versions) - [ -n "$VIASH_PAR_MULTIQC_VERSIONS" ] && ViashError Bad arguments for option \'--multiqc_versions\': \'$VIASH_PAR_MULTIQC_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MULTIQC_VERSIONS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --multiqc_versions. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --multiqc_versions=*) - [ -n "$VIASH_PAR_MULTIQC_VERSIONS" ] && ViashError Bad arguments for option \'--multiqc_versions=*\': \'$VIASH_PAR_MULTIQC_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_MULTIQC_VERSIONS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --versions) - [ -n "$VIASH_PAR_VERSIONS" ] && ViashError Bad arguments for option \'--versions\': \'$VIASH_PAR_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_VERSIONS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --versions. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --versions=*) - [ -n "$VIASH_PAR_VERSIONS" ] && ViashError Bad arguments for option \'--versions=*\': \'$VIASH_PAR_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_PAR_VERSIONS=$(ViashRemoveFlags "$1") - shift 1 - ;; - ---engine) - VIASH_ENGINE_ID="$2" - shift 2 - ;; - ---engine=*) - VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")" - shift 1 - ;; - ---cpus) - [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_META_CPUS="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - ---cpus=*) - [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_META_CPUS=$(ViashRemoveFlags "$1") - shift 1 - ;; - ---memory) - [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_META_MEMORY="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - ---memory=*) - [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 - VIASH_META_MEMORY=$(ViashRemoveFlags "$1") - shift 1 - ;; - *) # positional arg or unknown option - # since the positional args will be eval'd, can we always quote, instead of using ViashQuote - VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" - [[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters. - shift # past argument - ;; - esac -done - -# parse positional parameters -eval set -- $VIASH_POSITIONAL_ARGS - - -if [ "$VIASH_ENGINE_ID" == "native" ] ; then - VIASH_ENGINE_TYPE='native' -else - ViashError "Engine '$VIASH_ENGINE_ID' is not recognized. Options are: native." - exit 1 -fi - -# setting computational defaults - -# helper function for parsing memory strings -function ViashMemoryAsBytes { - local memory=`echo "$1" | tr '[:upper:]' '[:lower:]' | tr -d '[:space:]'` - local memory_regex='^([0-9]+)([kmgtp]i?b?|b)$' - if [[ $memory =~ $memory_regex ]]; then - local number=${memory/[^0-9]*/} - local symbol=${memory/*[0-9]/} - - case $symbol in - b) memory_b=$number ;; - kb|k) memory_b=$(( $number * 1000 )) ;; - mb|m) memory_b=$(( $number * 1000 * 1000 )) ;; - gb|g) memory_b=$(( $number * 1000 * 1000 * 1000 )) ;; - tb|t) memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 )) ;; - pb|p) memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 * 1000 )) ;; - kib|ki) memory_b=$(( $number * 1024 )) ;; - mib|mi) memory_b=$(( $number * 1024 * 1024 )) ;; - gib|gi) memory_b=$(( $number * 1024 * 1024 * 1024 )) ;; - tib|ti) memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 )) ;; - pib|pi) memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 * 1024 )) ;; - esac - echo "$memory_b" - fi -} -# compute memory in different units -if [ ! -z ${VIASH_META_MEMORY+x} ]; then - VIASH_META_MEMORY_B=`ViashMemoryAsBytes $VIASH_META_MEMORY` - # do not define other variables if memory_b is an empty string - if [ ! -z "$VIASH_META_MEMORY_B" ]; then - VIASH_META_MEMORY_KB=$(( ($VIASH_META_MEMORY_B+999) / 1000 )) - VIASH_META_MEMORY_MB=$(( ($VIASH_META_MEMORY_KB+999) / 1000 )) - VIASH_META_MEMORY_GB=$(( ($VIASH_META_MEMORY_MB+999) / 1000 )) - VIASH_META_MEMORY_TB=$(( ($VIASH_META_MEMORY_GB+999) / 1000 )) - VIASH_META_MEMORY_PB=$(( ($VIASH_META_MEMORY_TB+999) / 1000 )) - VIASH_META_MEMORY_KIB=$(( ($VIASH_META_MEMORY_B+1023) / 1024 )) - VIASH_META_MEMORY_MIB=$(( ($VIASH_META_MEMORY_KIB+1023) / 1024 )) - VIASH_META_MEMORY_GIB=$(( ($VIASH_META_MEMORY_MIB+1023) / 1024 )) - VIASH_META_MEMORY_TIB=$(( ($VIASH_META_MEMORY_GIB+1023) / 1024 )) - VIASH_META_MEMORY_PIB=$(( ($VIASH_META_MEMORY_TIB+1023) / 1024 )) - else - # unset memory if string is empty - unset $VIASH_META_MEMORY_B - fi -fi -# unset nproc if string is empty -if [ -z "$VIASH_META_CPUS" ]; then - unset $VIASH_META_CPUS -fi - - -# storing leftover values in positionals -if [[ $# -gt 0 ]]; then - VIASH_PAR_SKIP_DUPRADAR="$1" - shift 1 -fi -if [[ $# -gt 0 ]]; then - VIASH_PAR_SKIP_RSEQC="$1" - shift 1 -fi -if [[ $# -gt 0 ]]; then - VIASH_PAR_SKIP_MULTIQC="$1" - shift 1 -fi - -# check whether required parameters exist -if [ -z ${VIASH_PAR_ID+x} ]; then - ViashError '--id' is a required argument. Use "--help" to get more information on the parameters. - exit 1 -fi -if [ -z ${VIASH_PAR_FASTQ_1+x} ]; then - ViashError '--fastq_1' is a required argument. Use "--help" to get more information on the parameters. - exit 1 -fi -if [ -z ${VIASH_PAR_FASTA+x} ]; then - ViashError '--fasta' is a required argument. Use "--help" to get more information on the parameters. - exit 1 -fi -if [ -z ${VIASH_META_NAME+x} ]; then - ViashError 'name' is a required argument. Use "--help" to get more information on the parameters. - exit 1 -fi -if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then - ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters. - exit 1 -fi -if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then - ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters. - exit 1 -fi -if [ -z ${VIASH_META_EXECUTABLE+x} ]; then - ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters. - exit 1 -fi -if [ -z ${VIASH_META_CONFIG+x} ]; then - ViashError 'config' is a required argument. Use "--help" to get more information on the parameters. - exit 1 -fi -if [ -z ${VIASH_META_TEMP_DIR+x} ]; then - ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters. - exit 1 -fi - -# filling in defaults -if [ -z ${VIASH_PAR_STRANDEDNESS+x} ]; then - VIASH_PAR_STRANDEDNESS="auto" -fi -if [ -z ${VIASH_PAR_GENCODE+x} ]; then - VIASH_PAR_GENCODE="false" -fi -if [ -z ${VIASH_PAR_GTF_EXTRA_ATTRIBUTES+x} ]; then - VIASH_PAR_GTF_EXTRA_ATTRIBUTES="gene_name" -fi -if [ -z ${VIASH_PAR_GTF_GROUP_FEATURES+x} ]; then - VIASH_PAR_GTF_GROUP_FEATURES="gene_id" -fi -if [ -z ${VIASH_PAR_FEATURECOUNTS_GROUP_TYPE+x} ]; then - VIASH_PAR_FEATURECOUNTS_GROUP_TYPE="gene_biotype" -fi -if [ -z ${VIASH_PAR_FEATURECOUNTS_FEATURE_TYPE+x} ]; then - VIASH_PAR_FEATURECOUNTS_FEATURE_TYPE="exon" -fi -if [ -z ${VIASH_PAR_TRIMMER+x} ]; then - VIASH_PAR_TRIMMER="trimgalore" -fi -if [ -z ${VIASH_PAR_MIN_TRIMMED_READS+x} ]; then - VIASH_PAR_MIN_TRIMMED_READS="10000" -fi -if [ -z ${VIASH_PAR_REMOVE_RIBO_RNA+x} ]; then - VIASH_PAR_REMOVE_RIBO_RNA="false" -fi -if [ -z ${VIASH_PAR_RIBO_DATABASE_MANIFEST+x} ]; then - VIASH_PAR_RIBO_DATABASE_MANIFEST="assets/rrna-db-defaults.txt" -fi -if [ -z ${VIASH_PAR_WITH_UMI+x} ]; then - VIASH_PAR_WITH_UMI="false" -fi -if [ -z ${VIASH_PAR_UMITOOLS_EXTRACT_METHOD+x} ]; then - VIASH_PAR_UMITOOLS_EXTRACT_METHOD="string" -fi -if [ -z ${VIASH_PAR_UMI_DISCARD_READ+x} ]; then - VIASH_PAR_UMI_DISCARD_READ="0" -fi -if [ -z ${VIASH_PAR_UMITOOLS_UMI_SEPARATOR+x} ]; then - VIASH_PAR_UMITOOLS_UMI_SEPARATOR="_" -fi -if [ -z ${VIASH_PAR_UMITOOLS_GROUPING_METHOD+x} ]; then - VIASH_PAR_UMITOOLS_GROUPING_METHOD="directional" -fi -if [ -z ${VIASH_PAR_UMI_DEDUP_STATS+x} ]; then - VIASH_PAR_UMI_DEDUP_STATS="false" -fi -if [ -z ${VIASH_PAR_ALIGNER+x} ]; then - VIASH_PAR_ALIGNER="star_salmon" -fi -if [ -z ${VIASH_PAR_PSEUDO_ALIGNER+x} ]; then - VIASH_PAR_PSEUDO_ALIGNER="salmon" -fi -if [ -z ${VIASH_PAR_PSEUDO_ALIGNER_KMER_SIZE+x} ]; then - VIASH_PAR_PSEUDO_ALIGNER_KMER_SIZE="31" -fi -if [ -z ${VIASH_PAR_BAM_CSI_INDEX+x} ]; then - VIASH_PAR_BAM_CSI_INDEX="false" -fi -if [ -z ${VIASH_PAR_EXTRA_SALMON_QUANT_ARGS+x} ]; then - VIASH_PAR_EXTRA_SALMON_QUANT_ARGS="-v" -fi -if [ -z ${VIASH_PAR_MIN_MAPPED_READS+x} ]; then - VIASH_PAR_MIN_MAPPED_READS="5" -fi -if [ -z ${VIASH_PAR_STRINGTIE_IGNORE_GTF+x} ]; then - VIASH_PAR_STRINGTIE_IGNORE_GTF="false" -fi -if [ -z ${VIASH_PAR_EXTRA_STRINGTIE_ARGS+x} ]; then - VIASH_PAR_EXTRA_STRINGTIE_ARGS="-v" -fi -if [ -z ${VIASH_PAR_SAVE_UNALIGNED+x} ]; then - VIASH_PAR_SAVE_UNALIGNED="false" -fi -if [ -z ${VIASH_PAR_SAVE_ALIGN_INTERMEDS+x} ]; then - VIASH_PAR_SAVE_ALIGN_INTERMEDS="false" -fi -if [ -z ${VIASH_PAR_SKIP_ALIGNMENT+x} ]; then - VIASH_PAR_SKIP_ALIGNMENT="false" -fi -if [ -z ${VIASH_PAR_SKIP_PSEUDO_ALIGNMENT+x} ]; then - VIASH_PAR_SKIP_PSEUDO_ALIGNMENT="false" -fi -if [ -z ${VIASH_PAR_EXTRA_RSEM_CALCULATE_EXPRESSION_ARGS+x} ]; then - VIASH_PAR_EXTRA_RSEM_CALCULATE_EXPRESSION_ARGS="--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1" -fi -if [ -z ${VIASH_PAR_SKIP_FASTQC+x} ]; then - VIASH_PAR_SKIP_FASTQC="false" -fi -if [ -z ${VIASH_PAR_SKIP_TRIMMING+x} ]; then - VIASH_PAR_SKIP_TRIMMING="false" -fi -if [ -z ${VIASH_PAR_SKIP_BBSPLIT+x} ]; then - VIASH_PAR_SKIP_BBSPLIT="false" -fi -if [ -z ${VIASH_PAR_SKIP_UMI_EXTRACT+x} ]; then - VIASH_PAR_SKIP_UMI_EXTRACT="false" -fi -if [ -z ${VIASH_PAR_SKIP_QC+x} ]; then - VIASH_PAR_SKIP_QC="false" -fi -if [ -z ${VIASH_PAR_SKIP_MARKDUPLICATES+x} ]; then - VIASH_PAR_SKIP_MARKDUPLICATES="false" -fi -if [ -z ${VIASH_PAR_SKIP_STRINGTIE+x} ]; then - VIASH_PAR_SKIP_STRINGTIE="false" -fi -if [ -z ${VIASH_PAR_SKIP_BIOTYPE_QC+x} ]; then - VIASH_PAR_SKIP_BIOTYPE_QC="false" -fi -if [ -z ${VIASH_PAR_SKIP_BIGWIG+x} ]; then - VIASH_PAR_SKIP_BIGWIG="false" -fi -if [ -z ${VIASH_PAR_SKIP_PRESEQ+x} ]; then - VIASH_PAR_SKIP_PRESEQ="false" -fi -if [ -z ${VIASH_PAR_SKIP_DESEQ2_QC+x} ]; then - VIASH_PAR_SKIP_DESEQ2_QC="false" -fi -if [ -z ${VIASH_PAR_SKIP_DUPRADAR+x} ]; then - VIASH_PAR_SKIP_DUPRADAR="false" -fi -if [ -z ${VIASH_PAR_SKIP_RSEQC+x} ]; then - VIASH_PAR_SKIP_RSEQC="false" -fi -if [ -z ${VIASH_PAR_SKIP_MULTIQC+x} ]; then - VIASH_PAR_SKIP_MULTIQC="false" -fi -if [ -z ${VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS+x} ]; then - VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS=" --record-count 1000000 --seed 1" -fi -if [ -z ${VIASH_PAR_EXTRA_PICARD_ARGS+x} ]; then - VIASH_PAR_EXTRA_PICARD_ARGS=" --ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp" -fi -if [ -z ${VIASH_PAR_EXTRA_BEDTOOLS_ARGS+x} ]; then - VIASH_PAR_EXTRA_BEDTOOLS_ARGS=" -split -du" -fi -if [ -z ${VIASH_PAR_EXTRA_FEATURECOUNTS_ARGS+x} ]; then - VIASH_PAR_EXTRA_FEATURECOUNTS_ARGS=" -B -C" -fi -if [ -z ${VIASH_PAR_EXTRA_PRESEQ_ARGS+x} ]; then - VIASH_PAR_EXTRA_PRESEQ_ARGS="-verbose -seed 1 -seg_len 100000000" -fi -if [ -z ${VIASH_PAR_PCA_HEADER_MULTIQC+x} ]; then - VIASH_PAR_PCA_HEADER_MULTIQC="assets/multiqc/deseq2_pca_header.txt" -fi -if [ -z ${VIASH_PAR_CLUSTERING_HEADER_MULTIQC+x} ]; then - VIASH_PAR_CLUSTERING_HEADER_MULTIQC="assets/multiqc/deseq2_clustering_header.txt" -fi -if [ -z ${VIASH_PAR_DESEQ2_VST+x} ]; then - VIASH_PAR_DESEQ2_VST="true" -fi -if [ -z ${VIASH_PAR_EXTRA_DESEQ2_ARGS+x} ]; then - VIASH_PAR_EXTRA_DESEQ2_ARGS="--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3" -fi -if [ -z ${VIASH_PAR_EXTRA_DESEQ2_ARGS2+x} ]; then - VIASH_PAR_EXTRA_DESEQ2_ARGS2="star_salmon" -fi -if [ -z ${VIASH_PAR_RSEQC_MODULES+x} ]; then - VIASH_PAR_RSEQC_MODULES="bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication" -fi -if [ -z ${VIASH_PAR_MULTIQC_CUSTOM_CONFIG+x} ]; then - VIASH_PAR_MULTIQC_CUSTOM_CONFIG="assets/multiqc_config.yml" -fi -if [ -z ${VIASH_PAR_MULTIQC_METHODS_DESCRIPTION+x} ]; then - VIASH_PAR_MULTIQC_METHODS_DESCRIPTION="assets/methods_description_template.yml" -fi -if [ -z ${VIASH_PAR_OUTPUT_FASTA+x} ]; then - VIASH_PAR_OUTPUT_FASTA="genome/reference_genome.fasta" -fi -if [ -z ${VIASH_PAR_OUTPUT_GTF+x} ]; then - VIASH_PAR_OUTPUT_GTF="genome/gene_annotation.gtf" -fi -if [ -z ${VIASH_PAR_OUTPUT_TRANSCRIPT_FASTA+x} ]; then - VIASH_PAR_OUTPUT_TRANSCRIPT_FASTA="genome/transcriptome.fasta" -fi -if [ -z ${VIASH_PAR_OUTPUT_GENE_BED+x} ]; then - VIASH_PAR_OUTPUT_GENE_BED="genome/gene_annotation.bed" -fi -if [ -z ${VIASH_PAR_OUTPUT_STAR_INDEX+x} ]; then - VIASH_PAR_OUTPUT_STAR_INDEX="genome/index/STAR" -fi -if [ -z ${VIASH_PAR_OUTPUT_SALMON_INDEX+x} ]; then - VIASH_PAR_OUTPUT_SALMON_INDEX="genome/index/Salmon" -fi -if [ -z ${VIASH_PAR_OUTPUT_BBSPLIT_INDEX+x} ]; then - VIASH_PAR_OUTPUT_BBSPLIT_INDEX="genome/index/BBSplit" -fi -if [ -z ${VIASH_PAR_OUTPUT_KALLISTO_INDEX+x} ]; then - VIASH_PAR_OUTPUT_KALLISTO_INDEX="genome/index/Kallisto" -fi -if [ -z ${VIASH_PAR_OUTPUT_FASTQ_1+x} ]; then - VIASH_PAR_OUTPUT_FASTQ_1="fastq/\$id.read_1.fastq" -fi -if [ -z ${VIASH_PAR_OUTPUT_FASTQ_2+x} ]; then - VIASH_PAR_OUTPUT_FASTQ_2="fastq/\$id.read_2.fastq" -fi -if [ -z ${VIASH_PAR_FASTQC_HTML_1+x} ]; then - VIASH_PAR_FASTQC_HTML_1="fastqc_raw/\$id.read_1.fastqc.html" -fi -if [ -z ${VIASH_PAR_FASTQC_HTML_2+x} ]; then - VIASH_PAR_FASTQC_HTML_2="fastqc_raw/\$id.read_2.fastqc.html" -fi -if [ -z ${VIASH_PAR_FASTQC_ZIP_1+x} ]; then - VIASH_PAR_FASTQC_ZIP_1="fastqc_raw/\$id.read_1.fastqc.zip" -fi -if [ -z ${VIASH_PAR_FASTQC_ZIP_2+x} ]; then - VIASH_PAR_FASTQC_ZIP_2="fastqc_raw/\$id.read_2.fastqc.zip" -fi -if [ -z ${VIASH_PAR_TRIM_LOG_1+x} ]; then - VIASH_PAR_TRIM_LOG_1="trimgalore/\$id.read_1.trimming_report.txt" -fi -if [ -z ${VIASH_PAR_TRIM_LOG_2+x} ]; then - VIASH_PAR_TRIM_LOG_2="trimgalore/\$id.read_2.trimming_report.txt" -fi -if [ -z ${VIASH_PAR_TRIM_HTML_1+x} ]; then - VIASH_PAR_TRIM_HTML_1="fastqc_trim/\$id.read_1.trimmed_fastqc.html" -fi -if [ -z ${VIASH_PAR_TRIM_HTML_2+x} ]; then - VIASH_PAR_TRIM_HTML_2="fastqc_trim/\$id.read_2.trimmed_fastqc.html" -fi -if [ -z ${VIASH_PAR_TRIM_ZIP_1+x} ]; then - VIASH_PAR_TRIM_ZIP_1="fastqc_trim/\$id.read_1.trimmed_fastqc.zip" -fi -if [ -z ${VIASH_PAR_TRIM_ZIP_2+x} ]; then - VIASH_PAR_TRIM_ZIP_2="fastqc_trim/\$id.read_2.trimmed_fastqc.zip" -fi -if [ -z ${VIASH_PAR_SORTMERNA_LOG+x} ]; then - VIASH_PAR_SORTMERNA_LOG="sortmerna/\$id.log" -fi -if [ -z ${VIASH_PAR_STAR_ALIGNMENT+x} ]; then - VIASH_PAR_STAR_ALIGNMENT="STAR_alignment/\$id" -fi -if [ -z ${VIASH_PAR_GENOME_BAM_SORTED+x} ]; then - VIASH_PAR_GENOME_BAM_SORTED="STAR_alignment/genome_processed/\$id.genome.bam" -fi -if [ -z ${VIASH_PAR_GENOME_BAM_INDEX+x} ]; then - VIASH_PAR_GENOME_BAM_INDEX="STAR_alignment/genome_processed/\$id.genome.bam.bai" -fi -if [ -z ${VIASH_PAR_GENOME_BAM_STATS+x} ]; then - VIASH_PAR_GENOME_BAM_STATS="samtools_stats/\$id.genome.stats" -fi -if [ -z ${VIASH_PAR_GENOME_BAM_FLAGSTAT+x} ]; then - VIASH_PAR_GENOME_BAM_FLAGSTAT="samtools_stats/\$id.genome.flagstat" -fi -if [ -z ${VIASH_PAR_GENOME_BAM_IDXSTATS+x} ]; then - VIASH_PAR_GENOME_BAM_IDXSTATS="samtools_stats/\$id.genome.idxstats" -fi -if [ -z ${VIASH_PAR_TRANSCRIPTOME_BAM+x} ]; then - VIASH_PAR_TRANSCRIPTOME_BAM="STAR_alignment/transcriptome_processed/\$id.transcriptome.bam" -fi -if [ -z ${VIASH_PAR_TRANSCRIPTOME_BAM_INDEX+x} ]; then - VIASH_PAR_TRANSCRIPTOME_BAM_INDEX="STAR_alignment/transcriptome_processed/\$id.transcriptome.bam.bai" -fi -if [ -z ${VIASH_PAR_TRANSCRIPTOME_BAM_STATS+x} ]; then - VIASH_PAR_TRANSCRIPTOME_BAM_STATS="samtools_stats/\$id.transcriptome.stats" -fi -if [ -z ${VIASH_PAR_TRANSCRIPTOME_BAM_FLAGSTAT+x} ]; then - VIASH_PAR_TRANSCRIPTOME_BAM_FLAGSTAT="samtools_stats/\$id.transcriptome.flagstat" -fi -if [ -z ${VIASH_PAR_TRANSCRIPTOME_BAM_IDXSTATS+x} ]; then - VIASH_PAR_TRANSCRIPTOME_BAM_IDXSTATS="samtools_stats/\$id.transcriptome.idxstats" -fi -if [ -z ${VIASH_PAR_SALMON_QUANT_RESULTS+x} ]; then - VIASH_PAR_SALMON_QUANT_RESULTS="salmon/\$id" -fi -if [ -z ${VIASH_PAR_TPM_GENE+x} ]; then - VIASH_PAR_TPM_GENE="salmon/gene_tpm.tsv" -fi -if [ -z ${VIASH_PAR_COUNTS_GENE+x} ]; then - VIASH_PAR_COUNTS_GENE="salmon/gene_counts.tsv" -fi -if [ -z ${VIASH_PAR_COUNTS_GENE_LENGTH_SCALED+x} ]; then - VIASH_PAR_COUNTS_GENE_LENGTH_SCALED="salmon/gene_counts_length_scaled.tsv" -fi -if [ -z ${VIASH_PAR_COUNTS_GENE_SCALED+x} ]; then - VIASH_PAR_COUNTS_GENE_SCALED="salmon/gene_counts_scaled.tsv" -fi -if [ -z ${VIASH_PAR_TPM_TRANSCRIPT+x} ]; then - VIASH_PAR_TPM_TRANSCRIPT="salmon/transcript_tpm.tsv" -fi -if [ -z ${VIASH_PAR_COUNTS_TRANSCRIPT+x} ]; then - VIASH_PAR_COUNTS_TRANSCRIPT="salmon/transcript_counts.tsv" -fi -if [ -z ${VIASH_PAR_SALMON_MERGED_SUMMARIZEDEXPERIMENT+x} ]; then - VIASH_PAR_SALMON_MERGED_SUMMARIZEDEXPERIMENT="salmon/summarizedexperiment" -fi -if [ -z ${VIASH_PAR_MARKDUPLICATES_METRICS+x} ]; then - VIASH_PAR_MARKDUPLICATES_METRICS="picard/\$id.sorted.MarkDuplicates.metrics.txt" -fi -if [ -z ${VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF+x} ]; then - VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF="stringtie/\$id.transcripts.gtf" -fi -if [ -z ${VIASH_PAR_STRINGTIE_COVERAGE_GTF+x} ]; then - VIASH_PAR_STRINGTIE_COVERAGE_GTF="stringtie/\$id.coverage.gtf" -fi -if [ -z ${VIASH_PAR_STRINGTIE_ABUNDANCE+x} ]; then - VIASH_PAR_STRINGTIE_ABUNDANCE="stringtie/\$id.gene_abundance.txt" -fi -if [ -z ${VIASH_PAR_STRINGTIE_BALLGOWN+x} ]; then - VIASH_PAR_STRINGTIE_BALLGOWN="stringtie/\$id.ballgown" -fi -if [ -z ${VIASH_PAR_FEATURECOUNTS+x} ]; then - VIASH_PAR_FEATURECOUNTS="featurecounts/\$id.featureCounts.txt" -fi -if [ -z ${VIASH_PAR_FEATURECOUNTS_SUMMARY+x} ]; then - VIASH_PAR_FEATURECOUNTS_SUMMARY="featurecounts/\$id.featureCounts.txt.summary" -fi -if [ -z ${VIASH_PAR_FEATURECOUNTS_MULTIQC+x} ]; then - VIASH_PAR_FEATURECOUNTS_MULTIQC="featurecounts/\$id.featureCounts_mqc.tsv" -fi -if [ -z ${VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC+x} ]; then - VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC="featurecounts/\$id.featureCounts_rrna_mqc.tsv" -fi -if [ -z ${VIASH_PAR_BEDGRAPH_FORWARD+x} ]; then - VIASH_PAR_BEDGRAPH_FORWARD="bedgraph/\$id.forward.bedgraph" -fi -if [ -z ${VIASH_PAR_BEDGRAPH_REVERSE+x} ]; then - VIASH_PAR_BEDGRAPH_REVERSE="bedgraph/\$id.reverse.bedgraph" -fi -if [ -z ${VIASH_PAR_BIGWIG_FORWARD+x} ]; then - VIASH_PAR_BIGWIG_FORWARD="bigwig/\$id.forward.bigwig" -fi -if [ -z ${VIASH_PAR_BIGWIG_REVERSE+x} ]; then - VIASH_PAR_BIGWIG_REVERSE="bigwig/\$id.reverse.bigwig" -fi -if [ -z ${VIASH_PAR_PRESEQ_OUTPUT+x} ]; then - VIASH_PAR_PRESEQ_OUTPUT="preseq/\$id.lc_extrap.txt" -fi -if [ -z ${VIASH_PAR_BAMSTAT_OUTPUT+x} ]; then - VIASH_PAR_BAMSTAT_OUTPUT="RSeQC/bamstat/\$id.mapping_quality.txt" -fi -if [ -z ${VIASH_PAR_STRANDEDNESS_OUTPUT+x} ]; then - VIASH_PAR_STRANDEDNESS_OUTPUT="RSeQC/inferexperiment/\$id.strandedness.txt" -fi -if [ -z ${VIASH_PAR_INNER_DIST_OUTPUT_STATS+x} ]; then - VIASH_PAR_INNER_DIST_OUTPUT_STATS="RSeQC/innerdistance/\$id.inner_distance.stats" -fi -if [ -z ${VIASH_PAR_INNER_DIST_OUTPUT_DIST+x} ]; then - VIASH_PAR_INNER_DIST_OUTPUT_DIST="RSeQC/innerdistance/txt/\$id.inner_distance.txt" -fi -if [ -z ${VIASH_PAR_INNER_DIST_OUTPUT_FREQ+x} ]; then - VIASH_PAR_INNER_DIST_OUTPUT_FREQ="RSeQC/innerdistance/txt/\$id.inner_distance_freq.txt" -fi -if [ -z ${VIASH_PAR_INNER_DIST_OUTPUT_PLOT+x} ]; then - VIASH_PAR_INNER_DIST_OUTPUT_PLOT="RSeQC/innerdistance/pdf/\$id.inner_distance_plot.pdf" -fi -if [ -z ${VIASH_PAR_INNER_DIST_OUTPUT_PLOT_R+x} ]; then - VIASH_PAR_INNER_DIST_OUTPUT_PLOT_R="RSeQC/innerdistance/rscript/\$id.inner_distance_plot.r" -fi -if [ -z ${VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_LOG+x} ]; then - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_LOG="RSeQC/junctionannotation/log/\$id.junction_annotation.log" -fi -if [ -z ${VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_PLOT_R+x} ]; then - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_PLOT_R="RSeQC/junctionannotation/rscript/\$id.junction_annotation_plot.r" -fi -if [ -z ${VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_BED+x} ]; then - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_BED="RSeQC/junctionannotation/bed/\$id.junction_annotation.bed" -fi -if [ -z ${VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_INTERACT+x} ]; then - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_INTERACT="RSeQC/junctionannotation/bed/\$id.junction_annotation.Interact.bed" -fi -if [ -z ${VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_SHEET+x} ]; then - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_SHEET="RSeQC/junctionannotation/xls/\$id.junction_annotation.xls" -fi -if [ -z ${VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_EVENTS_PLOT+x} ]; then - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_EVENTS_PLOT="RSeQC/junctionannotation/pdf/\$id.splice_events.pdf" -fi -if [ -z ${VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_JUNCTIONS_PLOT+x} ]; then - VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_JUNCTIONS_PLOT="RSeQC/junctionannotation/pdf/\$id.splice_junctions_plot.pdf" -fi -if [ -z ${VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT_R+x} ]; then - VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT_R="RSeQC/junctionsaturation/rscript/\$id.junction_saturation_plot.r" -fi -if [ -z ${VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT+x} ]; then - VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT="RSeQC/junctionsaturation/pdf/\$id.junction_saturation_plot.pdf" -fi -if [ -z ${VIASH_PAR_READ_DISTRIBUTION_OUTPUT+x} ]; then - VIASH_PAR_READ_DISTRIBUTION_OUTPUT="RSeQC/readdistribution/\$id.read_distribution.txt" -fi -if [ -z ${VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT_R+x} ]; then - VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT_R="RSeQC/readduplication/rscrpt/\$id.duplication_rate_plot.r" -fi -if [ -z ${VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT+x} ]; then - VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT="RSeQC/readduplication/pdf/\$id.duplication_rate_plot.pdf" -fi -if [ -z ${VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_MAPPING+x} ]; then - VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_MAPPING="RSeQC/readduplication/xls/\$id.duplication_rate_mapping.xls" -fi -if [ -z ${VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_SEQUENCE+x} ]; then - VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_SEQUENCE="RSeQC/readduplication/xls/\$id.duplication_rate_sequencing.xls" -fi -if [ -z ${VIASH_PAR_TIN_OUTPUT_SUMMARY+x} ]; then - VIASH_PAR_TIN_OUTPUT_SUMMARY="RSeQC/tin/txt/\$id.tin_summary.txt" -fi -if [ -z ${VIASH_PAR_TIN_OUTPUT_METRICS+x} ]; then - VIASH_PAR_TIN_OUTPUT_METRICS="RSeQC/tin/xls/\$id.tin.xls" -fi -if [ -z ${VIASH_PAR_DUPRADAR_OUTPUT_DUPMATRIX+x} ]; then - VIASH_PAR_DUPRADAR_OUTPUT_DUPMATRIX="dupradar/gene_data/\$id.dup_matrix.txt" -fi -if [ -z ${VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC+x} ]; then - VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC="dupradar/mqc_intercept/\$id.dup_intercept_mqc.txt" -fi -if [ -z ${VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_BOXPLOT+x} ]; then - VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_BOXPLOT="dupradar/box_plot/\$id.duprate_exp_boxplot.pdf" -fi -if [ -z ${VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSPLOT+x} ]; then - VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSPLOT="dupradar/scatter_plot/\$id.duprate_exp_densityplot.pdf" -fi -if [ -z ${VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC+x} ]; then - VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC="dupradar/density_curve/\$id.duprate_exp_density_curve_mqc.pdf" -fi -if [ -z ${VIASH_PAR_DUPRADAR_OUTPUT_EXPRESSION_HISTOGRAM+x} ]; then - VIASH_PAR_DUPRADAR_OUTPUT_EXPRESSION_HISTOGRAM="dupradar/histogram/\$id.expression_hist.pdf" -fi -if [ -z ${VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE+x} ]; then - VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE="dupradar/intercept_slope/\$id.intercept_slope.txt" -fi -if [ -z ${VIASH_PAR_QUALIMAP_OUTPUT_PDF+x} ]; then - VIASH_PAR_QUALIMAP_OUTPUT_PDF="qualimap/\$id.qualimap_output.pdf" -fi -if [ -z ${VIASH_PAR_QUALIMAP_OUTPUT_DIR+x} ]; then - VIASH_PAR_QUALIMAP_OUTPUT_DIR="qualimap/\$id" -fi -if [ -z ${VIASH_PAR_DESEQ2_OUTPUT+x} ]; then - VIASH_PAR_DESEQ2_OUTPUT="deseq2_qc" -fi -if [ -z ${VIASH_PAR_MULTIQC_REPORT+x} ]; then - VIASH_PAR_MULTIQC_REPORT="multiqc/multiqc_report.html" -fi -if [ -z ${VIASH_PAR_MULTIQC_DATA+x} ]; then - VIASH_PAR_MULTIQC_DATA="multiqc/multiqc_data" -fi -if [ -z ${VIASH_PAR_MULTIQC_PLOTS+x} ]; then - VIASH_PAR_MULTIQC_PLOTS="multiqc/multiqc_plots" -fi - -# check whether required files exist -if [ ! -z "$VIASH_PAR_FASTQ_1" ]; then - IFS=';' - set -f - for file in $VIASH_PAR_FASTQ_1; do - unset IFS - if [ ! -e "$file" ]; then - ViashError "Input file '$file' does not exist." - exit 1 - fi - done - set +f -fi -if [ ! -z "$VIASH_PAR_FASTA" ] && [ ! -e "$VIASH_PAR_FASTA" ]; then - ViashError "Input file '$VIASH_PAR_FASTA' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_GTF" ] && [ ! -e "$VIASH_PAR_GTF" ]; then - ViashError "Input file '$VIASH_PAR_GTF' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_GFF" ] && [ ! -e "$VIASH_PAR_GFF" ]; then - ViashError "Input file '$VIASH_PAR_GFF' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_ADDITIONAL_FASTA" ] && [ ! -e "$VIASH_PAR_ADDITIONAL_FASTA" ]; then - ViashError "Input file '$VIASH_PAR_ADDITIONAL_FASTA' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_TRANSCRIPT_FASTA" ] && [ ! -e "$VIASH_PAR_TRANSCRIPT_FASTA" ]; then - ViashError "Input file '$VIASH_PAR_TRANSCRIPT_FASTA' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_GENE_BED" ] && [ ! -e "$VIASH_PAR_GENE_BED" ]; then - ViashError "Input file '$VIASH_PAR_GENE_BED' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_SPLICESITES" ] && [ ! -e "$VIASH_PAR_SPLICESITES" ]; then - ViashError "Input file '$VIASH_PAR_SPLICESITES' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_STAR_INDEX" ] && [ ! -e "$VIASH_PAR_STAR_INDEX" ]; then - ViashError "Input file '$VIASH_PAR_STAR_INDEX' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_RSEM_INDEX" ] && [ ! -e "$VIASH_PAR_RSEM_INDEX" ]; then - ViashError "Input file '$VIASH_PAR_RSEM_INDEX' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_SALMON_INDEX" ] && [ ! -e "$VIASH_PAR_SALMON_INDEX" ]; then - ViashError "Input file '$VIASH_PAR_SALMON_INDEX' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_KALLISTO_INDEX" ] && [ ! -e "$VIASH_PAR_KALLISTO_INDEX" ]; then - ViashError "Input file '$VIASH_PAR_KALLISTO_INDEX' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_BBSPLIT_FASTA_LIST" ] && [ ! -e "$VIASH_PAR_BBSPLIT_FASTA_LIST" ]; then - ViashError "Input file '$VIASH_PAR_BBSPLIT_FASTA_LIST' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_BBSPLIT_INDEX" ] && [ ! -e "$VIASH_PAR_BBSPLIT_INDEX" ]; then - ViashError "Input file '$VIASH_PAR_BBSPLIT_INDEX' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ] && [ ! -e "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ]; then - ViashError "Input file '$VIASH_PAR_RIBO_DATABASE_MANIFEST' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_PCA_HEADER_MULTIQC" ] && [ ! -e "$VIASH_PAR_PCA_HEADER_MULTIQC" ]; then - ViashError "Input file '$VIASH_PAR_PCA_HEADER_MULTIQC' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ] && [ ! -e "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ]; then - ViashError "Input file '$VIASH_PAR_CLUSTERING_HEADER_MULTIQC' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_MULTIQC_CUSTOM_CONFIG" ] && [ ! -e "$VIASH_PAR_MULTIQC_CUSTOM_CONFIG" ]; then - ViashError "Input file '$VIASH_PAR_MULTIQC_CUSTOM_CONFIG' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_MULTIQC_METHODS_DESCRIPTION" ] && [ ! -e "$VIASH_PAR_MULTIQC_METHODS_DESCRIPTION" ]; then - ViashError "Input file '$VIASH_PAR_MULTIQC_METHODS_DESCRIPTION' does not exist." - exit 1 -fi - -# check whether parameters values are of the right type -if [[ -n "$VIASH_PAR_GENCODE" ]]; then - if ! [[ "$VIASH_PAR_GENCODE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--gencode' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_MIN_TRIMMED_READS" ]]; then - if ! [[ "$VIASH_PAR_MIN_TRIMMED_READS" =~ ^[-+]?[0-9]+$ ]]; then - ViashError '--min_trimmed_reads' has to be an integer. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_REMOVE_RIBO_RNA" ]]; then - if ! [[ "$VIASH_PAR_REMOVE_RIBO_RNA" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--remove_ribo_rna' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_WITH_UMI" ]]; then - if ! [[ "$VIASH_PAR_WITH_UMI" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--with_umi' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_UMI_DISCARD_READ" ]]; then - if ! [[ "$VIASH_PAR_UMI_DISCARD_READ" =~ ^[-+]?[0-9]+$ ]]; then - ViashError '--umi_discard_read' has to be an integer. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_UMI_DEDUP_STATS" ]]; then - if ! [[ "$VIASH_PAR_UMI_DEDUP_STATS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--umi_dedup_stats' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_PSEUDO_ALIGNER_KMER_SIZE" ]]; then - if ! [[ "$VIASH_PAR_PSEUDO_ALIGNER_KMER_SIZE" =~ ^[-+]?[0-9]+$ ]]; then - ViashError '--pseudo_aligner_kmer_size' has to be an integer. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" ]]; then - if ! [[ "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then - ViashError '--kallisto_quant_fragment_length' has to be an integer. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" ]]; then - if ! [[ "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" =~ ^[-+]?[0-9]+$ ]]; then - ViashError '--kallisto_quant_fragment_length_sd' has to be an integer. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_BAM_CSI_INDEX" ]]; then - if ! [[ "$VIASH_PAR_BAM_CSI_INDEX" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--bam_csi_index' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_MIN_MAPPED_READS" ]]; then - if ! [[ "$VIASH_PAR_MIN_MAPPED_READS" =~ ^[-+]?[0-9]+$ ]]; then - ViashError '--min_mapped_reads' has to be an integer. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_STRINGTIE_IGNORE_GTF" ]]; then - if ! [[ "$VIASH_PAR_STRINGTIE_IGNORE_GTF" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--stringtie_ignore_gtf' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_SAVE_UNALIGNED" ]]; then - if ! [[ "$VIASH_PAR_SAVE_UNALIGNED" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--save_unaligned' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_SAVE_ALIGN_INTERMEDS" ]]; then - if ! [[ "$VIASH_PAR_SAVE_ALIGN_INTERMEDS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--save_align_intermeds' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_SKIP_ALIGNMENT" ]]; then - if ! [[ "$VIASH_PAR_SKIP_ALIGNMENT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--skip_alignment' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_SKIP_PSEUDO_ALIGNMENT" ]]; then - if ! [[ "$VIASH_PAR_SKIP_PSEUDO_ALIGNMENT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--skip_pseudo_alignment' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_SKIP_FASTQC" ]]; then - if ! [[ "$VIASH_PAR_SKIP_FASTQC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--skip_fastqc' has to be a boolean. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_SKIP_TRIMMING" ]]; then - if ! [[ "$VIASH_PAR_SKIP_TRIMMING" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--skip_trimming' has to be a boolean. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_SKIP_BBSPLIT" ]]; then - if ! [[ "$VIASH_PAR_SKIP_BBSPLIT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--skip_bbsplit' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_SKIP_UMI_EXTRACT" ]]; then - if ! [[ "$VIASH_PAR_SKIP_UMI_EXTRACT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--skip_umi_extract' has to be a boolean. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_SKIP_QC" ]]; then - if ! [[ "$VIASH_PAR_SKIP_QC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--skip_qc' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_SKIP_MARKDUPLICATES" ]]; then - if ! [[ "$VIASH_PAR_SKIP_MARKDUPLICATES" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--skip_markduplicates' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_SKIP_STRINGTIE" ]]; then - if ! [[ "$VIASH_PAR_SKIP_STRINGTIE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--skip_stringtie' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_SKIP_BIOTYPE_QC" ]]; then - if ! [[ "$VIASH_PAR_SKIP_BIOTYPE_QC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--skip_biotype_qc' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_SKIP_BIGWIG" ]]; then - if ! [[ "$VIASH_PAR_SKIP_BIGWIG" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--skip_bigwig' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_SKIP_PRESEQ" ]]; then - if ! [[ "$VIASH_PAR_SKIP_PRESEQ" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--skip_preseq' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_SKIP_DESEQ2_QC" ]]; then - if ! [[ "$VIASH_PAR_SKIP_DESEQ2_QC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--skip_deseq2_qc' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_SKIP_DUPRADAR" ]]; then - if ! [[ "$VIASH_PAR_SKIP_DUPRADAR" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError 'skip_dupradar' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_SKIP_RSEQC" ]]; then - if ! [[ "$VIASH_PAR_SKIP_RSEQC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError 'skip_rseqc' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_SKIP_MULTIQC" ]]; then - if ! [[ "$VIASH_PAR_SKIP_MULTIQC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError 'skip_multiqc' has to be a boolean_true. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_PAR_DESEQ2_VST" ]]; then - if ! [[ "$VIASH_PAR_DESEQ2_VST" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--deseq2_vst' has to be a boolean. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_META_CPUS" ]]; then - if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then - ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_META_MEMORY_B" ]]; then - if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then - ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_META_MEMORY_KB" ]]; then - if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then - ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_META_MEMORY_MB" ]]; then - if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then - ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_META_MEMORY_GB" ]]; then - if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then - ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_META_MEMORY_TB" ]]; then - if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then - ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_META_MEMORY_PB" ]]; then - if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then - ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then - if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then - ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then - if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then - ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then - if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then - ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then - if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then - ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters. - exit 1 - fi -fi -if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then - if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then - ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters. - exit 1 - fi -fi - -# check whether value is belongs to a set of choices -if [ ! -z "$VIASH_PAR_STRANDEDNESS" ]; then - VIASH_PAR_STRANDEDNESS_CHOICES=("unstranded;forward;reverse;auto") - IFS=';' - set -f - if ! [[ ";${VIASH_PAR_STRANDEDNESS_CHOICES[*]};" =~ ";$VIASH_PAR_STRANDEDNESS;" ]]; then - ViashError '--strandedness' specified value of \'$VIASH_PAR_STRANDEDNESS\' is not in the list of allowed values. Use "--help" to get more information on the parameters. - exit 1 - fi - set +f - unset IFS -fi - -if [ ! -z "$VIASH_PAR_TRIMMER" ]; then - VIASH_PAR_TRIMMER_CHOICES=("trimgalore;fastp") - IFS=';' - set -f - if ! [[ ";${VIASH_PAR_TRIMMER_CHOICES[*]};" =~ ";$VIASH_PAR_TRIMMER;" ]]; then - ViashError '--trimmer' specified value of \'$VIASH_PAR_TRIMMER\' is not in the list of allowed values. Use "--help" to get more information on the parameters. - exit 1 - fi - set +f - unset IFS -fi - -if [ ! -z "$VIASH_PAR_UMITOOLS_EXTRACT_METHOD" ]; then - VIASH_PAR_UMITOOLS_EXTRACT_METHOD_CHOICES=("string;regex") - IFS=';' - set -f - if ! [[ ";${VIASH_PAR_UMITOOLS_EXTRACT_METHOD_CHOICES[*]};" =~ ";$VIASH_PAR_UMITOOLS_EXTRACT_METHOD;" ]]; then - ViashError '--umitools_extract_method' specified value of \'$VIASH_PAR_UMITOOLS_EXTRACT_METHOD\' is not in the list of allowed values. Use "--help" to get more information on the parameters. - exit 1 - fi - set +f - unset IFS -fi - -if [ ! -z "$VIASH_PAR_UMI_DISCARD_READ" ]; then - VIASH_PAR_UMI_DISCARD_READ_CHOICES=("0;1;2") - IFS=';' - set -f - if ! [[ ";${VIASH_PAR_UMI_DISCARD_READ_CHOICES[*]};" =~ ";$VIASH_PAR_UMI_DISCARD_READ;" ]]; then - ViashError '--umi_discard_read' specified value of \'$VIASH_PAR_UMI_DISCARD_READ\' is not in the list of allowed values. Use "--help" to get more information on the parameters. - exit 1 - fi - set +f - unset IFS -fi - -if [ ! -z "$VIASH_PAR_UMITOOLS_GROUPING_METHOD" ]; then - VIASH_PAR_UMITOOLS_GROUPING_METHOD_CHOICES=("unique;percentile;cluster;adjacency;directional") - IFS=';' - set -f - if ! [[ ";${VIASH_PAR_UMITOOLS_GROUPING_METHOD_CHOICES[*]};" =~ ";$VIASH_PAR_UMITOOLS_GROUPING_METHOD;" ]]; then - ViashError '--umitools_grouping_method' specified value of \'$VIASH_PAR_UMITOOLS_GROUPING_METHOD\' is not in the list of allowed values. Use "--help" to get more information on the parameters. - exit 1 - fi - set +f - unset IFS -fi - -if [ ! -z "$VIASH_PAR_ALIGNER" ]; then - VIASH_PAR_ALIGNER_CHOICES=("star_salmon;star_rsem;hisat2") - IFS=';' - set -f - if ! [[ ";${VIASH_PAR_ALIGNER_CHOICES[*]};" =~ ";$VIASH_PAR_ALIGNER;" ]]; then - ViashError '--aligner' specified value of \'$VIASH_PAR_ALIGNER\' is not in the list of allowed values. Use "--help" to get more information on the parameters. - exit 1 - fi - set +f - unset IFS -fi - -if [ ! -z "$VIASH_PAR_PSEUDO_ALIGNER" ]; then - VIASH_PAR_PSEUDO_ALIGNER_CHOICES=("salmon;kallisto") - IFS=';' - set -f - if ! [[ ";${VIASH_PAR_PSEUDO_ALIGNER_CHOICES[*]};" =~ ";$VIASH_PAR_PSEUDO_ALIGNER;" ]]; then - ViashError '--pseudo_aligner' specified value of \'$VIASH_PAR_PSEUDO_ALIGNER\' is not in the list of allowed values. Use "--help" to get more information on the parameters. - exit 1 - fi - set +f - unset IFS -fi - -if [ ! -z "$VIASH_PAR_RSEQC_MODULES" ]; then - VIASH_PAR_RSEQC_MODULES_CHOICES=("bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication,tin") - IFS=',' - set -f - for val in $VIASH_PAR_RSEQC_MODULES; do - if ! [[ ",${VIASH_PAR_RSEQC_MODULES_CHOICES[*]}," =~ ",${val}," ]]; then - ViashError '--rseqc_modules' specified value of \'${val}\' is not in the list of allowed values. Use "--help" to get more information on the parameters. - exit 1 - fi - done - set +f - unset IFS -fi - -# create parent directories of output files, if so desired -if [ ! -z "$VIASH_PAR_OUTPUT_FASTA" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_FASTA")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_FASTA")" -fi -if [ ! -z "$VIASH_PAR_OUTPUT_GTF" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_GTF")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_GTF")" -fi -if [ ! -z "$VIASH_PAR_OUTPUT_TRANSCRIPT_FASTA" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_TRANSCRIPT_FASTA")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_TRANSCRIPT_FASTA")" -fi -if [ ! -z "$VIASH_PAR_OUTPUT_GENE_BED" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_GENE_BED")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_GENE_BED")" -fi -if [ ! -z "$VIASH_PAR_OUTPUT_STAR_INDEX" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_STAR_INDEX")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_STAR_INDEX")" -fi -if [ ! -z "$VIASH_PAR_OUTPUT_SALMON_INDEX" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_SALMON_INDEX")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_SALMON_INDEX")" -fi -if [ ! -z "$VIASH_PAR_OUTPUT_BBSPLIT_INDEX" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_BBSPLIT_INDEX")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_BBSPLIT_INDEX")" -fi -if [ ! -z "$VIASH_PAR_OUTPUT_KALLISTO_INDEX" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_KALLISTO_INDEX")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_KALLISTO_INDEX")" -fi -if [ ! -z "$VIASH_PAR_OUTPUT_FASTQ_1" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_FASTQ_1")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_FASTQ_1")" -fi -if [ ! -z "$VIASH_PAR_OUTPUT_FASTQ_2" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_FASTQ_2")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_FASTQ_2")" -fi -if [ ! -z "$VIASH_PAR_FASTQC_HTML_1" ] && [ ! -d "$(dirname "$VIASH_PAR_FASTQC_HTML_1")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_FASTQC_HTML_1")" -fi -if [ ! -z "$VIASH_PAR_FASTQC_HTML_2" ] && [ ! -d "$(dirname "$VIASH_PAR_FASTQC_HTML_2")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_FASTQC_HTML_2")" -fi -if [ ! -z "$VIASH_PAR_FASTQC_ZIP_1" ] && [ ! -d "$(dirname "$VIASH_PAR_FASTQC_ZIP_1")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_FASTQC_ZIP_1")" -fi -if [ ! -z "$VIASH_PAR_FASTQC_ZIP_2" ] && [ ! -d "$(dirname "$VIASH_PAR_FASTQC_ZIP_2")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_FASTQC_ZIP_2")" -fi -if [ ! -z "$VIASH_PAR_TRIM_LOG_1" ] && [ ! -d "$(dirname "$VIASH_PAR_TRIM_LOG_1")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_TRIM_LOG_1")" -fi -if [ ! -z "$VIASH_PAR_TRIM_LOG_2" ] && [ ! -d "$(dirname "$VIASH_PAR_TRIM_LOG_2")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_TRIM_LOG_2")" -fi -if [ ! -z "$VIASH_PAR_TRIM_HTML_1" ] && [ ! -d "$(dirname "$VIASH_PAR_TRIM_HTML_1")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_TRIM_HTML_1")" -fi -if [ ! -z "$VIASH_PAR_TRIM_HTML_2" ] && [ ! -d "$(dirname "$VIASH_PAR_TRIM_HTML_2")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_TRIM_HTML_2")" -fi -if [ ! -z "$VIASH_PAR_TRIM_ZIP_1" ] && [ ! -d "$(dirname "$VIASH_PAR_TRIM_ZIP_1")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_TRIM_ZIP_1")" -fi -if [ ! -z "$VIASH_PAR_TRIM_ZIP_2" ] && [ ! -d "$(dirname "$VIASH_PAR_TRIM_ZIP_2")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_TRIM_ZIP_2")" -fi -if [ ! -z "$VIASH_PAR_SORTMERNA_LOG" ] && [ ! -d "$(dirname "$VIASH_PAR_SORTMERNA_LOG")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_SORTMERNA_LOG")" -fi -if [ ! -z "$VIASH_PAR_STAR_ALIGNMENT" ] && [ ! -d "$(dirname "$VIASH_PAR_STAR_ALIGNMENT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_STAR_ALIGNMENT")" -fi -if [ ! -z "$VIASH_PAR_GENOME_BAM_SORTED" ] && [ ! -d "$(dirname "$VIASH_PAR_GENOME_BAM_SORTED")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_GENOME_BAM_SORTED")" -fi -if [ ! -z "$VIASH_PAR_GENOME_BAM_INDEX" ] && [ ! -d "$(dirname "$VIASH_PAR_GENOME_BAM_INDEX")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_GENOME_BAM_INDEX")" -fi -if [ ! -z "$VIASH_PAR_GENOME_BAM_STATS" ] && [ ! -d "$(dirname "$VIASH_PAR_GENOME_BAM_STATS")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_GENOME_BAM_STATS")" -fi -if [ ! -z "$VIASH_PAR_GENOME_BAM_FLAGSTAT" ] && [ ! -d "$(dirname "$VIASH_PAR_GENOME_BAM_FLAGSTAT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_GENOME_BAM_FLAGSTAT")" -fi -if [ ! -z "$VIASH_PAR_GENOME_BAM_IDXSTATS" ] && [ ! -d "$(dirname "$VIASH_PAR_GENOME_BAM_IDXSTATS")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_GENOME_BAM_IDXSTATS")" -fi -if [ ! -z "$VIASH_PAR_TRANSCRIPTOME_BAM" ] && [ ! -d "$(dirname "$VIASH_PAR_TRANSCRIPTOME_BAM")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_TRANSCRIPTOME_BAM")" -fi -if [ ! -z "$VIASH_PAR_TRANSCRIPTOME_BAM_INDEX" ] && [ ! -d "$(dirname "$VIASH_PAR_TRANSCRIPTOME_BAM_INDEX")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_TRANSCRIPTOME_BAM_INDEX")" -fi -if [ ! -z "$VIASH_PAR_TRANSCRIPTOME_BAM_STATS" ] && [ ! -d "$(dirname "$VIASH_PAR_TRANSCRIPTOME_BAM_STATS")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_TRANSCRIPTOME_BAM_STATS")" -fi -if [ ! -z "$VIASH_PAR_TRANSCRIPTOME_BAM_FLAGSTAT" ] && [ ! -d "$(dirname "$VIASH_PAR_TRANSCRIPTOME_BAM_FLAGSTAT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_TRANSCRIPTOME_BAM_FLAGSTAT")" -fi -if [ ! -z "$VIASH_PAR_TRANSCRIPTOME_BAM_IDXSTATS" ] && [ ! -d "$(dirname "$VIASH_PAR_TRANSCRIPTOME_BAM_IDXSTATS")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_TRANSCRIPTOME_BAM_IDXSTATS")" -fi -if [ ! -z "$VIASH_PAR_SALMON_QUANT_RESULTS" ] && [ ! -d "$(dirname "$VIASH_PAR_SALMON_QUANT_RESULTS")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_SALMON_QUANT_RESULTS")" -fi -if [ ! -z "$VIASH_PAR_TPM_GENE" ] && [ ! -d "$(dirname "$VIASH_PAR_TPM_GENE")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_TPM_GENE")" -fi -if [ ! -z "$VIASH_PAR_COUNTS_GENE" ] && [ ! -d "$(dirname "$VIASH_PAR_COUNTS_GENE")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_COUNTS_GENE")" -fi -if [ ! -z "$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED" ] && [ ! -d "$(dirname "$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED")" -fi -if [ ! -z "$VIASH_PAR_COUNTS_GENE_SCALED" ] && [ ! -d "$(dirname "$VIASH_PAR_COUNTS_GENE_SCALED")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_COUNTS_GENE_SCALED")" -fi -if [ ! -z "$VIASH_PAR_TPM_TRANSCRIPT" ] && [ ! -d "$(dirname "$VIASH_PAR_TPM_TRANSCRIPT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_TPM_TRANSCRIPT")" -fi -if [ ! -z "$VIASH_PAR_COUNTS_TRANSCRIPT" ] && [ ! -d "$(dirname "$VIASH_PAR_COUNTS_TRANSCRIPT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_COUNTS_TRANSCRIPT")" -fi -if [ ! -z "$VIASH_PAR_SALMON_MERGED_SUMMARIZEDEXPERIMENT" ] && [ ! -d "$(dirname "$VIASH_PAR_SALMON_MERGED_SUMMARIZEDEXPERIMENT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_SALMON_MERGED_SUMMARIZEDEXPERIMENT")" -fi -if [ ! -z "$VIASH_PAR_MARKDUPLICATES_METRICS" ] && [ ! -d "$(dirname "$VIASH_PAR_MARKDUPLICATES_METRICS")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_MARKDUPLICATES_METRICS")" -fi -if [ ! -z "$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF" ] && [ ! -d "$(dirname "$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF")" -fi -if [ ! -z "$VIASH_PAR_STRINGTIE_COVERAGE_GTF" ] && [ ! -d "$(dirname "$VIASH_PAR_STRINGTIE_COVERAGE_GTF")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_STRINGTIE_COVERAGE_GTF")" -fi -if [ ! -z "$VIASH_PAR_STRINGTIE_ABUNDANCE" ] && [ ! -d "$(dirname "$VIASH_PAR_STRINGTIE_ABUNDANCE")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_STRINGTIE_ABUNDANCE")" -fi -if [ ! -z "$VIASH_PAR_STRINGTIE_BALLGOWN" ] && [ ! -d "$(dirname "$VIASH_PAR_STRINGTIE_BALLGOWN")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_STRINGTIE_BALLGOWN")" -fi -if [ ! -z "$VIASH_PAR_FEATURECOUNTS" ] && [ ! -d "$(dirname "$VIASH_PAR_FEATURECOUNTS")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_FEATURECOUNTS")" -fi -if [ ! -z "$VIASH_PAR_FEATURECOUNTS_SUMMARY" ] && [ ! -d "$(dirname "$VIASH_PAR_FEATURECOUNTS_SUMMARY")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_FEATURECOUNTS_SUMMARY")" -fi -if [ ! -z "$VIASH_PAR_FEATURECOUNTS_MULTIQC" ] && [ ! -d "$(dirname "$VIASH_PAR_FEATURECOUNTS_MULTIQC")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_FEATURECOUNTS_MULTIQC")" -fi -if [ ! -z "$VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC" ] && [ ! -d "$(dirname "$VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC")" -fi -if [ ! -z "$VIASH_PAR_BEDGRAPH_FORWARD" ] && [ ! -d "$(dirname "$VIASH_PAR_BEDGRAPH_FORWARD")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_BEDGRAPH_FORWARD")" -fi -if [ ! -z "$VIASH_PAR_BEDGRAPH_REVERSE" ] && [ ! -d "$(dirname "$VIASH_PAR_BEDGRAPH_REVERSE")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_BEDGRAPH_REVERSE")" -fi -if [ ! -z "$VIASH_PAR_BIGWIG_FORWARD" ] && [ ! -d "$(dirname "$VIASH_PAR_BIGWIG_FORWARD")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_BIGWIG_FORWARD")" -fi -if [ ! -z "$VIASH_PAR_BIGWIG_REVERSE" ] && [ ! -d "$(dirname "$VIASH_PAR_BIGWIG_REVERSE")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_BIGWIG_REVERSE")" -fi -if [ ! -z "$VIASH_PAR_PRESEQ_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_PRESEQ_OUTPUT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_PRESEQ_OUTPUT")" -fi -if [ ! -z "$VIASH_PAR_BAMSTAT_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_BAMSTAT_OUTPUT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_BAMSTAT_OUTPUT")" -fi -if [ ! -z "$VIASH_PAR_STRANDEDNESS_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_STRANDEDNESS_OUTPUT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_STRANDEDNESS_OUTPUT")" -fi -if [ ! -z "$VIASH_PAR_INNER_DIST_OUTPUT_STATS" ] && [ ! -d "$(dirname "$VIASH_PAR_INNER_DIST_OUTPUT_STATS")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_INNER_DIST_OUTPUT_STATS")" -fi -if [ ! -z "$VIASH_PAR_INNER_DIST_OUTPUT_DIST" ] && [ ! -d "$(dirname "$VIASH_PAR_INNER_DIST_OUTPUT_DIST")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_INNER_DIST_OUTPUT_DIST")" -fi -if [ ! -z "$VIASH_PAR_INNER_DIST_OUTPUT_FREQ" ] && [ ! -d "$(dirname "$VIASH_PAR_INNER_DIST_OUTPUT_FREQ")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_INNER_DIST_OUTPUT_FREQ")" -fi -if [ ! -z "$VIASH_PAR_INNER_DIST_OUTPUT_PLOT" ] && [ ! -d "$(dirname "$VIASH_PAR_INNER_DIST_OUTPUT_PLOT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_INNER_DIST_OUTPUT_PLOT")" -fi -if [ ! -z "$VIASH_PAR_INNER_DIST_OUTPUT_PLOT_R" ] && [ ! -d "$(dirname "$VIASH_PAR_INNER_DIST_OUTPUT_PLOT_R")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_INNER_DIST_OUTPUT_PLOT_R")" -fi -if [ ! -z "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_LOG" ] && [ ! -d "$(dirname "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_LOG")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_LOG")" -fi -if [ ! -z "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_PLOT_R" ] && [ ! -d "$(dirname "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_PLOT_R")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_PLOT_R")" -fi -if [ ! -z "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_BED" ] && [ ! -d "$(dirname "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_BED")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_BED")" -fi -if [ ! -z "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_INTERACT" ] && [ ! -d "$(dirname "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_INTERACT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_INTERACT")" -fi -if [ ! -z "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_SHEET" ] && [ ! -d "$(dirname "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_SHEET")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_SHEET")" -fi -if [ ! -z "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_EVENTS_PLOT" ] && [ ! -d "$(dirname "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_EVENTS_PLOT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_EVENTS_PLOT")" -fi -if [ ! -z "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_JUNCTIONS_PLOT" ] && [ ! -d "$(dirname "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_JUNCTIONS_PLOT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_JUNCTIONS_PLOT")" -fi -if [ ! -z "$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT_R" ] && [ ! -d "$(dirname "$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT_R")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT_R")" -fi -if [ ! -z "$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT" ] && [ ! -d "$(dirname "$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT")" -fi -if [ ! -z "$VIASH_PAR_READ_DISTRIBUTION_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_READ_DISTRIBUTION_OUTPUT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_READ_DISTRIBUTION_OUTPUT")" -fi -if [ ! -z "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT_R" ] && [ ! -d "$(dirname "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT_R")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT_R")" -fi -if [ ! -z "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT" ] && [ ! -d "$(dirname "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT")" -fi -if [ ! -z "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_MAPPING" ] && [ ! -d "$(dirname "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_MAPPING")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_MAPPING")" -fi -if [ ! -z "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_SEQUENCE" ] && [ ! -d "$(dirname "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_SEQUENCE")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_SEQUENCE")" -fi -if [ ! -z "$VIASH_PAR_TIN_OUTPUT_SUMMARY" ] && [ ! -d "$(dirname "$VIASH_PAR_TIN_OUTPUT_SUMMARY")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_TIN_OUTPUT_SUMMARY")" -fi -if [ ! -z "$VIASH_PAR_TIN_OUTPUT_METRICS" ] && [ ! -d "$(dirname "$VIASH_PAR_TIN_OUTPUT_METRICS")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_TIN_OUTPUT_METRICS")" -fi -if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUPMATRIX" ] && [ ! -d "$(dirname "$VIASH_PAR_DUPRADAR_OUTPUT_DUPMATRIX")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_DUPRADAR_OUTPUT_DUPMATRIX")" -fi -if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC" ] && [ ! -d "$(dirname "$VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC")" -fi -if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_BOXPLOT" ] && [ ! -d "$(dirname "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_BOXPLOT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_BOXPLOT")" -fi -if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSPLOT" ] && [ ! -d "$(dirname "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSPLOT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSPLOT")" -fi -if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC" ] && [ ! -d "$(dirname "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC")" -fi -if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_EXPRESSION_HISTOGRAM" ] && [ ! -d "$(dirname "$VIASH_PAR_DUPRADAR_OUTPUT_EXPRESSION_HISTOGRAM")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_DUPRADAR_OUTPUT_EXPRESSION_HISTOGRAM")" -fi -if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE" ] && [ ! -d "$(dirname "$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE")" -fi -if [ ! -z "$VIASH_PAR_QUALIMAP_OUTPUT_PDF" ] && [ ! -d "$(dirname "$VIASH_PAR_QUALIMAP_OUTPUT_PDF")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_QUALIMAP_OUTPUT_PDF")" -fi -if [ ! -z "$VIASH_PAR_QUALIMAP_OUTPUT_DIR" ] && [ ! -d "$(dirname "$VIASH_PAR_QUALIMAP_OUTPUT_DIR")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_QUALIMAP_OUTPUT_DIR")" -fi -if [ ! -z "$VIASH_PAR_DESEQ2_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_DESEQ2_OUTPUT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_DESEQ2_OUTPUT")" -fi -if [ ! -z "$VIASH_PAR_MULTIQC_REPORT" ] && [ ! -d "$(dirname "$VIASH_PAR_MULTIQC_REPORT")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_MULTIQC_REPORT")" -fi -if [ ! -z "$VIASH_PAR_MULTIQC_DATA" ] && [ ! -d "$(dirname "$VIASH_PAR_MULTIQC_DATA")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_MULTIQC_DATA")" -fi -if [ ! -z "$VIASH_PAR_MULTIQC_PLOTS" ] && [ ! -d "$(dirname "$VIASH_PAR_MULTIQC_PLOTS")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_MULTIQC_PLOTS")" -fi -if [ ! -z "$VIASH_PAR_MULTIQC_VERSIONS" ] && [ ! -d "$(dirname "$VIASH_PAR_MULTIQC_VERSIONS")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_MULTIQC_VERSIONS")" -fi -if [ ! -z "$VIASH_PAR_VERSIONS" ] && [ ! -d "$(dirname "$VIASH_PAR_VERSIONS")" ]; then - mkdir -p "$(dirname "$VIASH_PAR_VERSIONS")" -fi - -if [ "$VIASH_ENGINE_ID" == "native" ] ; then - if [ "$VIASH_MODE" == "run" ]; then - VIASH_CMD="bash" - else - ViashError "Engine '$VIASH_ENGINE_ID' does not support mode '$VIASH_MODE'." - exit 1 - fi -fi - - -# set dependency paths -VIASH_DEP_WORKFLOWS_PREPARE_GENOME="$VIASH_META_RESOURCES_DIR/../../../nextflow/workflows/prepare_genome/main.nf" -VIASH_DEP_CAT_FASTQ="$VIASH_META_RESOURCES_DIR/../../../nextflow/cat_fastq/main.nf" -VIASH_DEP_WORKFLOWS_PRE_PROCESSING="$VIASH_META_RESOURCES_DIR/../../../nextflow/workflows/pre_processing/main.nf" -VIASH_DEP_WORKFLOWS_GENOME_ALIGNMENT_AND_QUANT="$VIASH_META_RESOURCES_DIR/../../../nextflow/workflows/genome_alignment_and_quant/main.nf" -VIASH_DEP_WORKFLOWS_PSEUDO_ALIGNMENT_AND_QUANT="$VIASH_META_RESOURCES_DIR/../../../nextflow/workflows/pseudo_alignment_and_quant/main.nf" -VIASH_DEP_WORKFLOWS_POST_PROCESSING="$VIASH_META_RESOURCES_DIR/../../../nextflow/workflows/post_processing/main.nf" -VIASH_DEP_WORKFLOWS_QUALITY_CONTROL="$VIASH_META_RESOURCES_DIR/../../../nextflow/workflows/quality_control/main.nf" - -ViashDebug "Running command: $(echo $VIASH_CMD)" -cat << VIASHEOF | eval $VIASH_CMD -set -e -tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-rnaseq-XXXXXX").nf -function clean_up { - rm "\$tempscript" -} -function interrupt { - echo -e "\nCTRL-C Pressed..." - exit 1 -} -trap clean_up EXIT -trap interrupt INT SIGINT -cat > "\$tempscript" << 'VIASHMAIN' -//// VIASH START -// The following code has been auto-generated by Viash. - -//// VIASH END -workflow run_wf { - take: - input_ch - - main: - reference_ch = input_ch - - | map { id, state -> - def biotype = state.gencode ? "gene_type" : state.featurecounts_group_type - def filter_gtf = - ( - ( !state.skip_alignment && state.aligner) // Condition 1: Alignment is required and aligner is set - || ( !state.skip_pseudo_alignment && state.pseudo_aligner ) // Condition 2: Pseudoalignment is required and pseudoaligner is set - || ( !state.transcript_fasta ) // Condition 3: Transcript FASTA file is not provided - ) - && - ( !state.skip_gtf_filter ) // Condition 4: --skip_gtf_filter is not provided - [ id, state + [ biotype: biotype, filter_gtf: filter_gtf ] ] - } - - | toSortedList - - | map { list -> - [ "ref", - [ fasta: list.collect { id, state -> state.fasta }.unique()[0], - gtf: list.collect { id, state -> state.gtf }.unique()[0], - gff: list.collect { id, state -> state.gff }.unique()[0], - additional_fasta: list.collect { id, state -> state.additional_fasta }.unique()[0], - transcript_fasta:list.collect { id, state -> state.transcript_fasta }.unique()[0], - gene_bed: list.collect { id, state -> state.gene_bed }.unique()[0], - bbsplit_fasta_list: list.collect { id, state -> state.bbsplit_fasta_list }.unique()[0], - aligner: list.collect { id, state -> state.aligner }.unique()[0], - pseudo_aligner: list.collect { id, state -> state.pseudo_aligner }.unique()[0], - star_index: list.collect { id, state -> state.star_index }.unique()[0], - rsem_index: list.collect { id, state -> state.rsem_index }.unique()[0], - salmon_index: list.collect { id, state -> state.salmon_index }.unique()[0], - kallisto_index: list.collect { id, state -> state.kallisto_index }.unique()[0], - // splicesites: list.collect { id, state -> state.splicesites }.unique()[0], - // hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0], - bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0], - skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0], - gencode: list.collect { id, state -> state.gencode }.unique()[0], - biotype: list.collect { id, state -> state.biotype }.unique()[0], - filter_gtf: list.collect { id, state -> state.filter_gtf }.unique()[0], - pseudo_aligner_kmer_size: list.collect { id, state -> state.pseudo_aligner_kmer_size }.unique()[0] ] - ] - } - - // prepare all the necessary files for reference genome - | prepare_genome.run ( - fromState: [ - "fasta": "fasta", - "gtf": "gtf", - "gff": "gff", - "additional_fasta": "additional_fasta", - "transcript_fasta": "transcript_fasta", - "gene_bed": "gene_bed", - "bbsplit_fasta_list": "bbsplit_fasta_list", - "star_index": "star_index", - "rsem_index": "rsem_index", - "salmon_index": "salmon_index", - "kallisto_index": "kallisto_index", - "pseudo_aligner_kmer_size": "pseudo_aligner_kmer_size", - // "splicesites": "splicesites", - // "hisat2_index": "hisat2_index", - "bbsplit_index": "bbsplit_index", - "skip_bbsplit": "skip_bbsplit", - "gencode": "gencode", - "biotype": "biotype", - "filter_gtf": "filter_gtf", - "aligner": "aligner", - "pseudo_aligner": "pseudo_aligner" - ], - toState: [ - "fasta": "uncompressed_fasta", - "gtf": "gtf_uncompressed", - "transcript_fasta": "transcript_fasta_uncompressed", - "fai": "fai", - "chrom_sizes": "chrom_sizes", - "bbsplit_index": "bbsplit_index_uncompressed", - "star_index": "star_index_uncompressed", - "salmon_index": "salmon_index_uncompressed", - "kallisto_index": "kallisto_index_uncompressed", - "gene_bed": "gene_bed_uncompressed" - ] - ) - - // Check if contigs in genome fasta file > 512 Mbp - | map { id, state -> - (isBelowMaxContigSize(state.fai)) ? [id, state] : [id, state + [bam_csi_index: true]] - } - - | map { list -> list[1]} - - analysis_ch = input_ch - - | combine(reference_ch) - - | map { list -> [list[0], list[1] + list[2]] } - - // Concatenate FastQ files from same sample if required - | cat_fastq.run ( - fromState: [ - "read_1": "fastq_1", - "read_2": "fastq_2" - ], - toState: [ - "fastq_1": "fastq_1", - "fastq_2": "fastq_2" - ] - ) - - // Pre-process fastq files - | pre_processing.run ( - fromState: [ - "id": "id", - "fastq_1": "fastq_1", - "fastq_2": "fastq_2", - "umitools_bc_pattern": "umitools_bc_pattern", - "umitools_bc_pattern2": "umitools_bc_pattern2", - "strandedness": "strandedness", - "transcript_fasta": "transcript_fasta", - "gtf": "gtf", - "with_umi": "with_umi", - "bbsplit_index": "bbsplit_index", - "bbsplit_fasta_list": "bbsplit_fasta_list", - "bc_pattern": "bc_pattern", - "ribo_database_manifest": "ribo_database_manifest", - "salmon_index": "salmon_index", - "skip_qc": "skip_qc", - "skip_fastqc": "skip_fastqc", - "skip_skip_umi_extract": "skip_umi_extract", - "umi_discard_read": "umi_discard_read", - "skip_trimming": "skip_trimming", - "trimmer": "trimmer", - "skip_bbsplit": "skip_bbsplit", - "remove_ribo_rna": "remove_ribo_rna" - ], - toState: [ - "fastqc_html_1": "fastqc_html_1", - "fastqc_html_2": "fastqc_html_2", - "fastqc_zip_1": "fastqc_zip_1", - "fastqc_zip_2": "fastqc_zip_2", - "fastq_1": "qc_output1", - "fastq_2": "qc_output2", - "trim_log_1": "trim_log_1", - "trim_log_2": "trim_log_2", - "trim_zip_1": "trim_zip_1", - "trim_zip_2": "trim_zip_2", - "trim_html_1": "trim_html_1", - "trim_html_2": "trim_html_2", - "passed_trimmed_reads": "passed_trimmed_reads", - "num_trimmed_reads": "num_trimmed_reads", - "sortmerna_log": "sortmerna_log", - "salmon_quant_output": "salmon_quant_output", - "fastp_failed_trim": "failed_trim", - "fastp_failed_trim_unpaired1": "failed_trim_unpaired1", - "fastp_failed_trim_unpaired2": "failed_trim_unpaired2", - "fastp_trim_json": "trim_json", - "fastp_trim_html": "trim_html", - "fastp_trim_merged_out": "trim_merged_out" - ] - ) - - // Infer strandedness from Salmon pseudo-alignment results - | map { id, state -> - (state.strandedness == 'auto') ? - [ id, state + [strandedness: getSalmonInferredStrandedness(state.salmon_quant_output)] ] : - [id, state] - } - - // Filter FastQ files based on minimum trimmed read count after adapter trimming - | map { id, state -> - def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ] - def num_reads = (state.skip_trimming) ? - state.min_trimmed_reads + 1 : - ( - (state.trimmer == "fastp") ? - getFastpReadsAfterFiltering(state.fastp_trim_json) : - ( - (!state.skip_trimming && input.size() == 2) ? - getTrimGaloreReadsAfterFiltering(state.trim_log_2) : - getTrimGaloreReadsAfterFiltering(state.trim_log_1) - ) - ) - def passed_trimmed_reads = - (state.skip_trimming || (num_reads >= state.min_trimmed_reads)) ? - true : - false - [ id, state + [num_trimmed_reads: num_reads, passed_trimmed_reads: passed_trimmed_reads] ] - } - - // Genome alignment and quantification - | genome_alignment_and_quant.run ( - runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads }, - fromState: [ - "id": "id", - "fastq_1": "fastq_1", - "fastq_2": "fastq_2", - "strandedness": "strandedness", - "gtf": "gtf", - "transcript_fasta": "transcript_fasta", - "bam_csi_index": "bam_csi_index", - "aligner": "aligner", - "rsem_index": "rsem_index", - "star_index": "star_index", - "extra_star_align_args": "extra_star_align_args", - "star_ignore_sjdbgtf": "star_ignore_sjdbgtf", - "seq_platform": "seq_platform", - "seq_center": "seq_center", - "with_umi": "with_umi", - "umi_dedup_stats": "umi_dedup_stats", - "gtf_group_features": "gtf_group_features", - "gtf_extra_attributes": "gtf_extra_attributes", - "salmon_quant_libtype": "salmon_quant_libtype", - "salmon_index": "salmon_index", - "extra_rsem_calculate_expression_args": "extra_rsem_calculate_expression_args" - ], - toState: [ - "star_alignment": "star_alignment", - "star_multiqc": "star_multiqc", - "genome_bam_sorted": "genome_bam_sorted", - "genome_bam_index": "genome_bam_index", - "genome_bam_stats": "genome_bam_stats", - "genome_bam_flagstat": "genome_bam_flagstat", - "genome_bam_idxstats": "genome_bam_idxstats", - "transcriptome_bam": "transcriptome_bam", - "transcriptome_bam_index": "transcriptome_bam_index", - "transcriptome_bam_stats": "transcriptome_bam_stats", - "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", - "transcriptome_bam_idxstats": "transcriptome_bam_idxstats", - "quant_out_dir": "quant_out_dir", - "quant_results_file": "quant_results_file" - ] - ) - - // Filter channels to get samples that passed STAR minimum mapping percentage - | map { id, state -> - def percent_mapped = getStarPercentMapped(state.star_multiqc) - def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false - [ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ] - } - - // Pseudo-alignment and quantification - | pseudo_alignment_and_quant.run ( - runIf: { id, state -> !state.skip_pseudo_alignment && state.passed_trimmed_reads }, - fromState: [ - "id": "id", - "fastq_1": "fastq_1", - "fastq_2": "fastq_2", - "strandedness": "strandedness", - "gtf": "gtf", - "transcript_fasta": "transcript_fasta", - "pseudo_aligner": "pseudo_aligner", - "salmon_index": "salmon_index", - "kallisto_index": "kallisto_index", - "extra_star_align_args": "extra_star_align_args", - "star_ignore_sjdbgtf": "star_ignore_sjdbgtf", - "seq_platform": "seq_platform", - "seq_center": "seq_center", - "with_umi": "with_umi", - "umi_dedup_stats": "umi_dedup_stats", - "gtf_group_features": "gtf_group_features", - "gtf_extra_attributes": "gtf_extra_attributes", - "lib_type": "salmon_quant_libtype", - "kallisto_quant_fragment_length": "kallisto_quant_fragment_length", - "kallisto_quant_fragment_length_sd": "kallisto_quant_fragment_length_sd" - ], - toState: [ - "pseudo_quant_out_dir": "quant_out_dir", - "pseudo_salmon_quant_results_file": "salmon_quant_results_file", - "pseudo_kallisto_quant_results_file": "kallisto_quant_results_file", - "pseudo_multiqc": "pseudo_multiqc" - ] - ) - - | map { id, state -> - def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ] - def paired = input.size() == 2 - [ id, state + [ paired: paired ] ] - } - - // Post-processing - | post_processing.run ( - runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads && state.passed_mapping }, - fromState: [ - "id": "id", - "paired": "paired", - "strandedness": "strandedness", - "fasta": "fasta", - "fai": "fai", - "gtf": "gtf", - "genome_bam": "genome_bam_sorted", - "chrom_sizes": "chrom_sizes", - "star_multiqc": "star_multiqc", - "extra_picard_args": "extra_picard_args", - "extra_stringtie_args": "extra_stringtie_args", - "stringtie_ignore_gtf": "stringtie_ignore_gtf", - "extra_bedtools_args": "extra_bedtools_args", - "bam_csi_index": "bam_csi_index", - "min_mapped_reads": "min_mapped_reads", - "with_umi": "with_umi", - "skip_qc": "skip_qc", - "skip_markduplicates": "skip_markduplicates", - "skip_stringtie": "skip_stringtie", - "skip_bigwig":"gencode" - ], - toState: [ - "genome_bam_sorted": "processed_genome_bam", - "genome_bam_index": "genome_bam_index", - "genome_bam_stats": "genome_bam_stats", - "genome_bam_flagstat": "genome_bam_flagstat", - "genome_bam_idxstats": "genome_bam_idxstats", - "markduplicates_metrics": "markduplicates_metrics", - "stringtie_transcript_gtf": "stringtie_transcript_gtf", - "stringtie_coverage_gtf": "stringtie_coverage_gtf", - "stringtie_abundance": "stringtie_abundance", - "stringtie_ballgown": "stringtie_ballgown", - "bedgraph_forward": "bedgraph_forward", - "bedgraph_reverse": "bedgraph_reverse", - "bigwig_forward": "bigwig_forward", - "bigwig_reverse": "bigwig_reverse" - ] - ) - - // Final QC - | quality_control.run ( - fromState: [ - "id": "id", - "paired": "paired", - "strandedness": "strandedness", - "skip_align": "skip_alignment", - "skip_pseudo_align": "skip_pseudo_alignment", - "gtf": "gtf", - "genome_bam": "genome_bam_sorted", - "genome_bam_index": "genome_bam_index", - "quant_out_dir": "quant_out_dir", - "quant_results_file": "quant_results_file", - "pseudo_quant_out_dir": "pseudo_quant_out_dir", - "pseudo_salmon_quant_results_file": "pseudo_salmon_quant_results_file", - "pseudo_kallisto_quant_results_file": "pseudo_kallisto_quant_results_file", - "aligner": "aligner", - "pseudo_aligner": "pseudo_aligner", - "pseudo_multiqc": "pseudo_multiqc", - "gene_bed": "gene_bed", - "extra_preseq_args": "extra_preseq_args", - "extra_featurecounts_args": "extra_featurecounts_args", - "biotype": "biotype", - "biotypes_header": "biotypes_header", - "skip_biotype_qc": "skip_biotype_qc", - "featurecounts_group_type": "featurecounts_group_type", - "featurecounts_feature_type": "featurecounts_feature_type", - "gencode": "gencode", - "skip_deseq2_qc": "skip_deseq2_qc", - "extra_deseq2_args": "extra_deseq2_args", - "extra_deseq2_args2": "extra_deseq2_args2", - "multiqc_custom_config": "multiqc_custom_config", - "multiqc_title": "multiqc_title", - "multiqc_methods_description": "multiqc_methods_description", - "fastqc_zip_1": "fastqc_zip_1", - "fastqc_zip_2": "fastqc_zip_2", - "trim_log_1": "trim_log_1", - "trim_log_2": "trim_log_2", - "trim_zip_1": "trim_zip_1", - "trim_zip_2": "trim_zip_2", - "sortmerna_multiqc": "sortmerna_log", - "star_multiqc": "star_multiqc", - "genome_bam_stats": "genome_bam_stats", - "genome_bam_flagstat": "genome_bam_flagstat", - "genome_bam_idxstats": "genome_bam_idxstats", - "markduplicates_multiqc": "markduplicates_metrics", - "rseqc_modules": "rseqc_modules", - "num_trimmed_reads": "num_trimmed_reads", - "passed_trimmed_reads": "passed_trimmed_reads", - "passed_mapping": "passed_mapping", - "percent_mapped": "percent_mapped" - ], - toState: [ - "preseq_output": "preseq_output", - "bamstat_output": "bamstat_output", - "strandedness_output": "strandedness_output", - "inner_dist_output_stats": "inner_dist_output_stats", - "inner_dist_output_dist": "inner_dist_output_dist", - "inner_dist_output_freq": "inner_dist_output_freq", - "inner_dist_output_plot": "inner_dist_output_plot", - "inner_dist_output_plot_r": "inner_dist_output_plot_r", - "junction_annotation_output_log": "junction_annotation_output_log", - "junction_annotation_output_plot_r": "junction_annotation_output_plot_r", - "junction_annotation_output_junction_bed": "junction_annotation_output_junction_bed", - "junction_annotation_output_junction_interact": "junction_annotation_output_junction_interact", - "junction_annotation_output_junction_sheet": "junction_annotation_output_junction_sheet", - "junction_annotation_output_splice_events_plot": "junction_annotation_output_splice_events_plot", - "junction_annotation_output_splice_junctions_plot": "junction_annotation_output_splice_junctions_plot", - "junction_saturation_output_plot_r": "junction_saturation_output_plot_r", - "junction_saturation_output_plot": "junction_saturation_output_plot", - "read_distribution_output": "read_distribution_output", - "read_duplication_output_duplication_rate_plot_r": "read_duplication_output_duplication_rate_plot_r", - "read_duplication_output_duplication_rate_plot": "read_duplication_output_duplication_rate_plot", - "read_duplication_output_duplication_rate_mapping": "read_duplication_output_duplication_rate_mapping", - "read_duplication_output_duplication_rate_sequence": "read_duplication_output_duplication_rate_sequence", - "tin_output_summary": "tin_output_summary", - "tin_output_metrics": "tin_output_metrics", - "dupradar_output_dupmatrix": "dupradar_output_dupmatrix", - "dupradar_output_dup_intercept_mqc": "dupradar_output_dup_intercept_mqc", - "dupradar_output_duprate_exp_boxplot": "dupradar_output_duprate_exp_boxplot", - "dupradar_output_duprate_exp_densplot": "dupradar_output_duprate_exp_densplot", - "dupradar_output_duprate_exp_denscurve_mqc": "dupradar_output_duprate_exp_denscurve_mqc", - "dupradar_output_expression_histogram": "dupradar_output_expression_histogram", - "dupradar_output_intercept_slope": "dupradar_output_intercept_slope", - "qualimap_output_dir": "qualimap_output_dir", - "qualimap_output_pdf": "qualimap_output_pdf", - "featurecounts": "featurecounts", - "featurecounts_summary": "featurecounts_summary", - "featurecounts_multiqc": "featurecounts_multiqc", - "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", - "tpm_gene": "tpm_gene", - "counts_gene": "counts_gene", - "counts_gene_length_scaled": "counts_gene_length_scaled", - "counts_gene_scaled": "counts_gene_scaled", - "tpm_transcript": "tpm_transcript", - "counts_transcript": "counts_transcript", - "salmon_merged_summarizedexperiment": "salmon_merged_summarizedexperiment", - "deseq2_output": "deseq2_output", - "multiqc_report": "multiqc_report", - "multiqc_data": "multiqc_data", - "multiqc_plots": "multiqc_plots" - ] - ) - - | map { id, state -> - def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } - [ id, mod_state ] - } - - | setState ( - [ - "output_fasta": "fasta", - "output_gtf": "gtf", - "output_transcript_fasta": "transcript_fasta", - "output_gene_bed": "gene_bed", - "output_bbsplit_index": "bbsplit_index", - "output_star_index": "star_index", - "output_salmon_index": "salmon_index", - "output_kallisto_index": "kallisto_index", - "fastqc_html_1": "fastqc_html_1", - "fastqc_html_2": "fastqc_html_2", - "fastqc_zip_1": "fastqc_zip_1", - "fastqc_zip_2": "fastqc_zip_2", - "output_fastq_1": "fastq_1", - "output_fastq_2": "fastq_2", - "trim_log_1": "trim_log_1", - "trim_log_2": "trim_log_2", - "trim_zip_1": "trim_zip_1", - "trim_zip_2": "trim_zip_2", - "trim_html_1": "trim_html_1", - "trim_html_2": "trim_html_2", - "sortmerna_log": "sortmerna_log", - "star_alignment": "star_alignment", - "genome_bam_sorted": "genome_bam_sorted", - "genome_bam_index": "genome_bam_index", - "genome_bam_stats": "samtools_stats", - "genome_bam_flagstat": "samtools_flagstat", - "genome_bam_idxstats": "samtools_idxstats", - "transcriptome_bam": "transcriptome_bam", - "transcriptome_bam_index": "transcriptome_bam_index", - "transcriptome_bam_stats": "transcriptome_bam_stats", - "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", - "transcriptome_bam_idxstats": "transcriptome_bam_idxstats", - "salmon_quant_results": "salmon_quant_results", - "stringtie_transcript_gtf": "stringtie_transcript_gtf", - "stringtie_coverage_gtf": "stringtie_coverage_gtf", - "stringtie_abundance": "stringtie_abundance", - "stringtie_ballgown": "stringtie_ballgown", - "featurecounts": "featurecounts", - "featurecounts_summary": "featurecounts_summary", - "featurecounts_multiqc": "featurecounts_multiqc", - "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", - "bedgraph_forward": "bedgraph_forward", - "bedgraph_reverse": "bedgraph_reverse", - "bigwig_forward": "bigwig_forward", - "bigwig_reverse": "bigwig_reverse", - "preseq_output": "preseq_output", - "bamstat_output": "bamstat_output", - "strandedness_output": "strandedness_output", - "inner_dist_output_stats": "inner_dist_output_stats", - "inner_dist_output_dist": "inner_dist_output_dist", - "inner_dist_output_freq": "inner_dist_output_freq", - "inner_dist_output_plot": "inner_dist_output_plot", - "inner_dist_output_plot_r": "inner_dist_output_plot_r", - "junction_annotation_output_log": "junction_annotation_output_log", - "junction_annotation_output_plot_r": "junction_annotation_output_plot_r", - "junction_annotation_output_junction_bed": "junction_annotation_output_junction_bed", - "junction_annotation_output_junction_interact": "junction_annotation_output_junction_interact", - "junction_annotation_output_junction_sheet": "junction_annotation_output_junction_sheet", - "junction_annotation_output_splice_events_plot": "junction_annotation_output_splice_events_plot", - "junction_annotation_output_splice_junctions_plot": "junction_annotation_output_splice_junctions_plot", - "junction_saturation_output_plot_r": "junction_saturation_output_plot_r", - "junction_saturation_output_plot": "junction_saturation_output_plot", - "read_distribution_output": "read_distribution_output", - "read_duplication_output_duplication_rate_plot_r": "read_duplication_output_duplication_rate_plot_r", - "read_duplication_output_duplication_rate_plot": "read_duplication_output_duplication_rate_plot", - "read_duplication_output_duplication_rate_mapping": "read_duplication_output_duplication_rate_mapping", - "read_duplication_output_duplication_rate_sequence": "read_duplication_output_duplication_rate_sequence", - "tin_output_summary": "tin_output_summary", - "tin_output_metrics": "tin_output_metrics", - "dupradar_output_dupmatrix": "dupradar_output_dupmatrix", - "dupradar_output_dup_intercept_mqc": "dupradar_output_dup_intercept_mqc", - "dupradar_output_duprate_exp_boxplot": "dupradar_output_duprate_exp_boxplot", - "dupradar_output_duprate_exp_densplot": "dupradar_output_duprate_exp_densplot", - "dupradar_output_duprate_exp_denscurve_mqc": "dupradar_output_duprate_exp_denscurve_mqc", - "dupradar_output_expression_histogram": "dupradar_output_expression_histogram", - "dupradar_output_intercept_slope": "dupradar_output_intercept_slope", - "qualimap_output_dir": "qualimap_output_dir", - "qualimap_output_pdf": "qualimap_output_pdf", - "tpm_gene": "tpm_gene", - "counts_gene": "counts_gene", - "counts_gene_length_scaled": "counts_gene_length_scaled", - "counts_gene_scaled": "counts_gene_scaled", - "tpm_transcript": "tpm_transcript", - "counts_transcript": "counts_transcript", - "quant_merged_summarizedexperiment": "quant_merged_summarizedexperiment", - "deseq2_output": "deseq2_output", - "pseudo_tpm_gene": "pseudo_tpm_gene", - "pseudo_counts_gene": "pseudo_counts_gene", - "pseudo_counts_gene_length_scaled": "pseudo_counts_gene_length_scaled", - "pseudo_counts_gene_scaled": "pseudo_counts_gene_scaled", - "pseudo_tpm_transcript": "pseudo_tpm_transcript", - "pseudo_counts_transcript": "pseudo_counts_transcript", - "pseudo_lengths_gene": "pseudo_lengths_gene", - "pseudo_lengths_transcript": "pseudo_lengths_transcript", - "pseudo_quant_merged_summarizedexperiment": "pseudo_quant_merged_summarizedexperiment", - "deseq2_output_pseudo": "deseq2_output_pseudo", - "multiqc_report": "multiqc_report", - "multiqc_data": "multiqc_data", - "multiqc_plots": "multiqc_plots", - "multiqc_versions": "multiqc_versions" - ] - ) - - output_ch = analysis_ch - - emit: - output_ch -} - -import nextflow.Nextflow -// -// Function to generate an error if contigs in genome fasta file > 512 Mbp -// -def isBelowMaxContigSize(fai_file) { - def max_size = 512000000 - fai_file.eachLine { line -> - def lspl = line.split('\\t') - def chrom = lspl[0] - def size = lspl[1] - if (size.toInteger() > max_size) { - def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\\n" + - " Contig longer than \${max_size}bp found in reference genome!\\n\\n" + - " \${chrom}: \${size}\\n\\n" + - " Provide the '--bam_csi_index' parameter to use a CSI instead of BAI index.\\n\\n" - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - Nextflow.error(error_string) - return false - } - } - return true -} - -import groovy.json.JsonSlurper -// -// Function that parses Salmon quant 'meta_info.json' output file to get inferred strandedness -// -def getSalmonInferredStrandedness(salmon_quant_output) { - def json_file = new File(salmon_quant_output).listFiles().find { it.name == "meta_info.json" || it.isDirectory() && it.listFiles().find { it.name == "meta_info.json" } } - def lib_type = new JsonSlurper().parseText(json_file.text).get('library_types')[0] - def strandedness = 'reverse' - if (lib_type) { - if (lib_type in ['U', 'IU']) { - strandedness = 'unstranded' - } - else if (lib_type in ['SF', 'ISF']) { - strandedness = 'forward' - } - else if (lib_type in ['SR', 'ISR']) { - strandedness = 'reverse' - } - } - return strandedness -} - -// -// Function that parses TrimGalore log output file to get total number of reads after trimming -// -def getTrimGaloreReadsAfterFiltering(log_file) { - def total_reads = 0 - def filtered_reads = 0 - log_file.eachLine { line -> - def total_reads_matcher = line =~ /([\\d\\.]+)\\ssequences processed in total/ - def filtered_reads_matcher = line =~ /shorter than the length cutoff[^:]+:\\s([\\d\\.]+)/ - if (total_reads_matcher) total_reads = total_reads_matcher[0][1].toFloat() - if (filtered_reads_matcher) filtered_reads = filtered_reads_matcher[0][1].toFloat() - } - return total_reads - filtered_reads -} - -// -// Function that parses fastp json output file to get total number of reads after trimming -// -def getFastpReadsAfterFiltering(json_file) { - def Map json = (Map) new JsonSlurper().parseText(json_file.text).get('summary') - return json['after_filtering']['total_reads'].toLong() -} - -// -// Function that parses and returns the alignment rate from the STAR log output -// -def getStarPercentMapped(align_log) { - def percent_aligned = 0 - def pattern = /Uniquely mapped reads %\\s*\\|\\s*([\\d\\.]+)%/ - align_log.eachLine { line -> - def matcher = line =~ pattern - if (matcher) { - percent_aligned = matcher[0][1].toFloat() - } - } - return percent_aligned -} -VIASHMAIN -nextflow run . -main-script "\$tempscript" & -wait "\$!" - -VIASHEOF - - -# check whether required files exist -if [ ! -z "$VIASH_PAR_OUTPUT_FASTA" ] && [ ! -e "$VIASH_PAR_OUTPUT_FASTA" ]; then - ViashError "Output file '$VIASH_PAR_OUTPUT_FASTA' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_OUTPUT_GTF" ] && [ ! -e "$VIASH_PAR_OUTPUT_GTF" ]; then - ViashError "Output file '$VIASH_PAR_OUTPUT_GTF' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_OUTPUT_TRANSCRIPT_FASTA" ] && [ ! -e "$VIASH_PAR_OUTPUT_TRANSCRIPT_FASTA" ]; then - ViashError "Output file '$VIASH_PAR_OUTPUT_TRANSCRIPT_FASTA' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_OUTPUT_GENE_BED" ] && [ ! -e "$VIASH_PAR_OUTPUT_GENE_BED" ]; then - ViashError "Output file '$VIASH_PAR_OUTPUT_GENE_BED' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_OUTPUT_STAR_INDEX" ] && [ ! -e "$VIASH_PAR_OUTPUT_STAR_INDEX" ]; then - ViashError "Output file '$VIASH_PAR_OUTPUT_STAR_INDEX' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_OUTPUT_SALMON_INDEX" ] && [ ! -e "$VIASH_PAR_OUTPUT_SALMON_INDEX" ]; then - ViashError "Output file '$VIASH_PAR_OUTPUT_SALMON_INDEX' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_OUTPUT_BBSPLIT_INDEX" ] && [ ! -e "$VIASH_PAR_OUTPUT_BBSPLIT_INDEX" ]; then - ViashError "Output file '$VIASH_PAR_OUTPUT_BBSPLIT_INDEX' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_OUTPUT_KALLISTO_INDEX" ] && [ ! -e "$VIASH_PAR_OUTPUT_KALLISTO_INDEX" ]; then - ViashError "Output file '$VIASH_PAR_OUTPUT_KALLISTO_INDEX' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_STAR_ALIGNMENT" ] && [ ! -e "$VIASH_PAR_STAR_ALIGNMENT" ]; then - ViashError "Output file '$VIASH_PAR_STAR_ALIGNMENT' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_GENOME_BAM_SORTED" ] && [ ! -e "$VIASH_PAR_GENOME_BAM_SORTED" ]; then - ViashError "Output file '$VIASH_PAR_GENOME_BAM_SORTED' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_GENOME_BAM_INDEX" ] && [ ! -e "$VIASH_PAR_GENOME_BAM_INDEX" ]; then - ViashError "Output file '$VIASH_PAR_GENOME_BAM_INDEX' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_GENOME_BAM_STATS" ] && [ ! -e "$VIASH_PAR_GENOME_BAM_STATS" ]; then - ViashError "Output file '$VIASH_PAR_GENOME_BAM_STATS' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_GENOME_BAM_FLAGSTAT" ] && [ ! -e "$VIASH_PAR_GENOME_BAM_FLAGSTAT" ]; then - ViashError "Output file '$VIASH_PAR_GENOME_BAM_FLAGSTAT' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_GENOME_BAM_IDXSTATS" ] && [ ! -e "$VIASH_PAR_GENOME_BAM_IDXSTATS" ]; then - ViashError "Output file '$VIASH_PAR_GENOME_BAM_IDXSTATS' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_TRANSCRIPTOME_BAM" ] && [ ! -e "$VIASH_PAR_TRANSCRIPTOME_BAM" ]; then - ViashError "Output file '$VIASH_PAR_TRANSCRIPTOME_BAM' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_TRANSCRIPTOME_BAM_INDEX" ] && [ ! -e "$VIASH_PAR_TRANSCRIPTOME_BAM_INDEX" ]; then - ViashError "Output file '$VIASH_PAR_TRANSCRIPTOME_BAM_INDEX' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_TRANSCRIPTOME_BAM_STATS" ] && [ ! -e "$VIASH_PAR_TRANSCRIPTOME_BAM_STATS" ]; then - ViashError "Output file '$VIASH_PAR_TRANSCRIPTOME_BAM_STATS' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_TRANSCRIPTOME_BAM_FLAGSTAT" ] && [ ! -e "$VIASH_PAR_TRANSCRIPTOME_BAM_FLAGSTAT" ]; then - ViashError "Output file '$VIASH_PAR_TRANSCRIPTOME_BAM_FLAGSTAT' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_TRANSCRIPTOME_BAM_IDXSTATS" ] && [ ! -e "$VIASH_PAR_TRANSCRIPTOME_BAM_IDXSTATS" ]; then - ViashError "Output file '$VIASH_PAR_TRANSCRIPTOME_BAM_IDXSTATS' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_SALMON_QUANT_RESULTS" ] && [ ! -e "$VIASH_PAR_SALMON_QUANT_RESULTS" ]; then - ViashError "Output file '$VIASH_PAR_SALMON_QUANT_RESULTS' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_TPM_GENE" ] && [ ! -e "$VIASH_PAR_TPM_GENE" ]; then - ViashError "Output file '$VIASH_PAR_TPM_GENE' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_COUNTS_GENE" ] && [ ! -e "$VIASH_PAR_COUNTS_GENE" ]; then - ViashError "Output file '$VIASH_PAR_COUNTS_GENE' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED" ] && [ ! -e "$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED" ]; then - ViashError "Output file '$VIASH_PAR_COUNTS_GENE_LENGTH_SCALED' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_COUNTS_GENE_SCALED" ] && [ ! -e "$VIASH_PAR_COUNTS_GENE_SCALED" ]; then - ViashError "Output file '$VIASH_PAR_COUNTS_GENE_SCALED' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_TPM_TRANSCRIPT" ] && [ ! -e "$VIASH_PAR_TPM_TRANSCRIPT" ]; then - ViashError "Output file '$VIASH_PAR_TPM_TRANSCRIPT' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_COUNTS_TRANSCRIPT" ] && [ ! -e "$VIASH_PAR_COUNTS_TRANSCRIPT" ]; then - ViashError "Output file '$VIASH_PAR_COUNTS_TRANSCRIPT' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_SALMON_MERGED_SUMMARIZEDEXPERIMENT" ] && [ ! -e "$VIASH_PAR_SALMON_MERGED_SUMMARIZEDEXPERIMENT" ]; then - ViashError "Output file '$VIASH_PAR_SALMON_MERGED_SUMMARIZEDEXPERIMENT' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_MARKDUPLICATES_METRICS" ] && [ ! -e "$VIASH_PAR_MARKDUPLICATES_METRICS" ]; then - ViashError "Output file '$VIASH_PAR_MARKDUPLICATES_METRICS' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF" ] && [ ! -e "$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF" ]; then - ViashError "Output file '$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_STRINGTIE_COVERAGE_GTF" ] && [ ! -e "$VIASH_PAR_STRINGTIE_COVERAGE_GTF" ]; then - ViashError "Output file '$VIASH_PAR_STRINGTIE_COVERAGE_GTF' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_STRINGTIE_ABUNDANCE" ] && [ ! -e "$VIASH_PAR_STRINGTIE_ABUNDANCE" ]; then - ViashError "Output file '$VIASH_PAR_STRINGTIE_ABUNDANCE' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_STRINGTIE_BALLGOWN" ] && [ ! -e "$VIASH_PAR_STRINGTIE_BALLGOWN" ]; then - ViashError "Output file '$VIASH_PAR_STRINGTIE_BALLGOWN' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_FEATURECOUNTS" ] && [ ! -e "$VIASH_PAR_FEATURECOUNTS" ]; then - ViashError "Output file '$VIASH_PAR_FEATURECOUNTS' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_FEATURECOUNTS_SUMMARY" ] && [ ! -e "$VIASH_PAR_FEATURECOUNTS_SUMMARY" ]; then - ViashError "Output file '$VIASH_PAR_FEATURECOUNTS_SUMMARY' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_BEDGRAPH_FORWARD" ] && [ ! -e "$VIASH_PAR_BEDGRAPH_FORWARD" ]; then - ViashError "Output file '$VIASH_PAR_BEDGRAPH_FORWARD' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_BEDGRAPH_REVERSE" ] && [ ! -e "$VIASH_PAR_BEDGRAPH_REVERSE" ]; then - ViashError "Output file '$VIASH_PAR_BEDGRAPH_REVERSE' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_BIGWIG_FORWARD" ] && [ ! -e "$VIASH_PAR_BIGWIG_FORWARD" ]; then - ViashError "Output file '$VIASH_PAR_BIGWIG_FORWARD' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_BIGWIG_REVERSE" ] && [ ! -e "$VIASH_PAR_BIGWIG_REVERSE" ]; then - ViashError "Output file '$VIASH_PAR_BIGWIG_REVERSE' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_PRESEQ_OUTPUT" ] && [ ! -e "$VIASH_PAR_PRESEQ_OUTPUT" ]; then - ViashError "Output file '$VIASH_PAR_PRESEQ_OUTPUT' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_BAMSTAT_OUTPUT" ] && [ ! -e "$VIASH_PAR_BAMSTAT_OUTPUT" ]; then - ViashError "Output file '$VIASH_PAR_BAMSTAT_OUTPUT' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_STRANDEDNESS_OUTPUT" ] && [ ! -e "$VIASH_PAR_STRANDEDNESS_OUTPUT" ]; then - ViashError "Output file '$VIASH_PAR_STRANDEDNESS_OUTPUT' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_LOG" ] && [ ! -e "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_LOG" ]; then - ViashError "Output file '$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_LOG' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_PLOT_R" ] && [ ! -e "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_PLOT_R" ]; then - ViashError "Output file '$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_PLOT_R' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_BED" ] && [ ! -e "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_BED" ]; then - ViashError "Output file '$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_BED' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_INTERACT" ] && [ ! -e "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_INTERACT" ]; then - ViashError "Output file '$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_INTERACT' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_SHEET" ] && [ ! -e "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_SHEET" ]; then - ViashError "Output file '$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_JUNCTION_SHEET' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_EVENTS_PLOT" ] && [ ! -e "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_EVENTS_PLOT" ]; then - ViashError "Output file '$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_EVENTS_PLOT' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_JUNCTIONS_PLOT" ] && [ ! -e "$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_JUNCTIONS_PLOT" ]; then - ViashError "Output file '$VIASH_PAR_JUNCTION_ANNOTATION_OUTPUT_SPLICE_JUNCTIONS_PLOT' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT_R" ] && [ ! -e "$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT_R" ]; then - ViashError "Output file '$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT_R' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT" ] && [ ! -e "$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT" ]; then - ViashError "Output file '$VIASH_PAR_JUNCTION_SATURATION_OUTPUT_PLOT' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_READ_DISTRIBUTION_OUTPUT" ] && [ ! -e "$VIASH_PAR_READ_DISTRIBUTION_OUTPUT" ]; then - ViashError "Output file '$VIASH_PAR_READ_DISTRIBUTION_OUTPUT' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT_R" ] && [ ! -e "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT_R" ]; then - ViashError "Output file '$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT_R' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT" ] && [ ! -e "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT" ]; then - ViashError "Output file '$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_PLOT' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_MAPPING" ] && [ ! -e "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_MAPPING" ]; then - ViashError "Output file '$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_MAPPING' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_SEQUENCE" ] && [ ! -e "$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_SEQUENCE" ]; then - ViashError "Output file '$VIASH_PAR_READ_DUPLICATION_OUTPUT_DUPLICATION_RATE_SEQUENCE' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_TIN_OUTPUT_SUMMARY" ] && [ ! -e "$VIASH_PAR_TIN_OUTPUT_SUMMARY" ]; then - ViashError "Output file '$VIASH_PAR_TIN_OUTPUT_SUMMARY' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_TIN_OUTPUT_METRICS" ] && [ ! -e "$VIASH_PAR_TIN_OUTPUT_METRICS" ]; then - ViashError "Output file '$VIASH_PAR_TIN_OUTPUT_METRICS' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUPMATRIX" ] && [ ! -e "$VIASH_PAR_DUPRADAR_OUTPUT_DUPMATRIX" ]; then - ViashError "Output file '$VIASH_PAR_DUPRADAR_OUTPUT_DUPMATRIX' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC" ] && [ ! -e "$VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC" ]; then - ViashError "Output file '$VIASH_PAR_DUPRADAR_OUTPUT_DUP_INTERCEPT_MQC' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_BOXPLOT" ] && [ ! -e "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_BOXPLOT" ]; then - ViashError "Output file '$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_BOXPLOT' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSPLOT" ] && [ ! -e "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSPLOT" ]; then - ViashError "Output file '$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSPLOT' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC" ] && [ ! -e "$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC" ]; then - ViashError "Output file '$VIASH_PAR_DUPRADAR_OUTPUT_DUPRATE_EXP_DENSCURVE_MQC' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_EXPRESSION_HISTOGRAM" ] && [ ! -e "$VIASH_PAR_DUPRADAR_OUTPUT_EXPRESSION_HISTOGRAM" ]; then - ViashError "Output file '$VIASH_PAR_DUPRADAR_OUTPUT_EXPRESSION_HISTOGRAM' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE" ] && [ ! -e "$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE" ]; then - ViashError "Output file '$VIASH_PAR_DUPRADAR_OUTPUT_INTERCEPT_SLOPE' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_QUALIMAP_OUTPUT_DIR" ] && [ ! -e "$VIASH_PAR_QUALIMAP_OUTPUT_DIR" ]; then - ViashError "Output file '$VIASH_PAR_QUALIMAP_OUTPUT_DIR' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_DESEQ2_OUTPUT" ] && [ ! -e "$VIASH_PAR_DESEQ2_OUTPUT" ]; then - ViashError "Output file '$VIASH_PAR_DESEQ2_OUTPUT' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_MULTIQC_REPORT" ] && [ ! -e "$VIASH_PAR_MULTIQC_REPORT" ]; then - ViashError "Output file '$VIASH_PAR_MULTIQC_REPORT' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_MULTIQC_DATA" ] && [ ! -e "$VIASH_PAR_MULTIQC_DATA" ]; then - ViashError "Output file '$VIASH_PAR_MULTIQC_DATA' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_MULTIQC_PLOTS" ] && [ ! -e "$VIASH_PAR_MULTIQC_PLOTS" ]; then - ViashError "Output file '$VIASH_PAR_MULTIQC_PLOTS' does not exist." - exit 1 -fi -if [ ! -z "$VIASH_PAR_MULTIQC_VERSIONS" ] && [ ! -e "$VIASH_PAR_MULTIQC_VERSIONS" ]; then - ViashError "Output file '$VIASH_PAR_MULTIQC_VERSIONS' does not exist." - exit 1 -fi - - -exit 0 diff --git a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml index 9860d0b..45cb37a 100644 --- a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml +++ b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml @@ -238,8 +238,8 @@ build_info: output: "target/nextflow/bbmap_bbsplit" executable: "target/nextflow/bbmap_bbsplit/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/bbmap_bbsplit/main.nf b/target/nextflow/bbmap_bbsplit/main.nf index 685dbdc..0fc6e1f 100644 --- a/target/nextflow/bbmap_bbsplit/main.nf +++ b/target/nextflow/bbmap_bbsplit/main.nf @@ -3104,8 +3104,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/bbmap_bbsplit", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/bedtools_genomecov/.config.vsh.yaml b/target/nextflow/bedtools_genomecov/.config.vsh.yaml index 223b434..21bbcfb 100644 --- a/target/nextflow/bedtools_genomecov/.config.vsh.yaml +++ b/target/nextflow/bedtools_genomecov/.config.vsh.yaml @@ -178,8 +178,8 @@ build_info: output: "target/nextflow/bedtools_genomecov" executable: "target/nextflow/bedtools_genomecov/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/bedtools_genomecov/main.nf b/target/nextflow/bedtools_genomecov/main.nf index 2654169..bff2361 100644 --- a/target/nextflow/bedtools_genomecov/main.nf +++ b/target/nextflow/bedtools_genomecov/main.nf @@ -3031,8 +3031,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/bedtools_genomecov", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/cat_additional_fasta/.config.vsh.yaml b/target/nextflow/cat_additional_fasta/.config.vsh.yaml index 143b36e..205d3da 100644 --- a/target/nextflow/cat_additional_fasta/.config.vsh.yaml +++ b/target/nextflow/cat_additional_fasta/.config.vsh.yaml @@ -182,8 +182,8 @@ build_info: output: "target/nextflow/cat_additional_fasta" executable: "target/nextflow/cat_additional_fasta/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/cat_additional_fasta/main.nf b/target/nextflow/cat_additional_fasta/main.nf index faea778..27c85b5 100644 --- a/target/nextflow/cat_additional_fasta/main.nf +++ b/target/nextflow/cat_additional_fasta/main.nf @@ -3032,8 +3032,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/cat_additional_fasta", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/cat_fastq/.config.vsh.yaml b/target/nextflow/cat_fastq/.config.vsh.yaml index 884e2db..ac6127a 100644 --- a/target/nextflow/cat_fastq/.config.vsh.yaml +++ b/target/nextflow/cat_fastq/.config.vsh.yaml @@ -169,8 +169,8 @@ build_info: output: "target/nextflow/cat_fastq" executable: "target/nextflow/cat_fastq/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/cat_fastq/main.nf b/target/nextflow/cat_fastq/main.nf index 1fb986a..9a356e0 100644 --- a/target/nextflow/cat_fastq/main.nf +++ b/target/nextflow/cat_fastq/main.nf @@ -3023,8 +3023,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/cat_fastq", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/deseq2_qc/.config.vsh.yaml b/target/nextflow/deseq2_qc/.config.vsh.yaml index 91f5d05..a0080ba 100644 --- a/target/nextflow/deseq2_qc/.config.vsh.yaml +++ b/target/nextflow/deseq2_qc/.config.vsh.yaml @@ -237,8 +237,8 @@ build_info: output: "target/nextflow/deseq2_qc" executable: "target/nextflow/deseq2_qc/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/deseq2_qc/main.nf b/target/nextflow/deseq2_qc/main.nf index 10d8217..cb40097 100644 --- a/target/nextflow/deseq2_qc/main.nf +++ b/target/nextflow/deseq2_qc/main.nf @@ -3110,8 +3110,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/deseq2_qc", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/dupradar/.config.vsh.yaml b/target/nextflow/dupradar/.config.vsh.yaml index 021d414..4125804 100644 --- a/target/nextflow/dupradar/.config.vsh.yaml +++ b/target/nextflow/dupradar/.config.vsh.yaml @@ -266,8 +266,8 @@ build_info: output: "target/nextflow/dupradar" executable: "target/nextflow/dupradar/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/dupradar/main.nf b/target/nextflow/dupradar/main.nf index d644c22..527f0fe 100644 --- a/target/nextflow/dupradar/main.nf +++ b/target/nextflow/dupradar/main.nf @@ -3136,8 +3136,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/dupradar", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/fastqc/.config.vsh.yaml b/target/nextflow/fastqc/.config.vsh.yaml index ba1bbd3..a4d57b5 100644 --- a/target/nextflow/fastqc/.config.vsh.yaml +++ b/target/nextflow/fastqc/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/nextflow/fastqc" executable: "target/nextflow/fastqc/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/fastqc/main.nf b/target/nextflow/fastqc/main.nf index f18b551..fe0dcc4 100644 --- a/target/nextflow/fastqc/main.nf +++ b/target/nextflow/fastqc/main.nf @@ -3056,8 +3056,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/fastqc", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/fq_subsample/.config.vsh.yaml b/target/nextflow/fq_subsample/.config.vsh.yaml index 4ce156f..ec1e172 100644 --- a/target/nextflow/fq_subsample/.config.vsh.yaml +++ b/target/nextflow/fq_subsample/.config.vsh.yaml @@ -177,8 +177,8 @@ build_info: output: "target/nextflow/fq_subsample" executable: "target/nextflow/fq_subsample/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/fq_subsample/main.nf b/target/nextflow/fq_subsample/main.nf index 25c7632..704614b 100644 --- a/target/nextflow/fq_subsample/main.nf +++ b/target/nextflow/fq_subsample/main.nf @@ -3027,8 +3027,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/fq_subsample", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/getchromsizes/.config.vsh.yaml b/target/nextflow/getchromsizes/.config.vsh.yaml index b709b9f..54ee944 100644 --- a/target/nextflow/getchromsizes/.config.vsh.yaml +++ b/target/nextflow/getchromsizes/.config.vsh.yaml @@ -167,8 +167,8 @@ build_info: output: "target/nextflow/getchromsizes" executable: "target/nextflow/getchromsizes/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/getchromsizes/main.nf b/target/nextflow/getchromsizes/main.nf index 497bed5..691d635 100644 --- a/target/nextflow/getchromsizes/main.nf +++ b/target/nextflow/getchromsizes/main.nf @@ -3013,8 +3013,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/getchromsizes", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/gtf2bed/.config.vsh.yaml b/target/nextflow/gtf2bed/.config.vsh.yaml index bbb9096..0e5d328 100644 --- a/target/nextflow/gtf2bed/.config.vsh.yaml +++ b/target/nextflow/gtf2bed/.config.vsh.yaml @@ -145,8 +145,8 @@ build_info: output: "target/nextflow/gtf2bed" executable: "target/nextflow/gtf2bed/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/gtf2bed/main.nf b/target/nextflow/gtf2bed/main.nf index 30849d3..2732c0d 100644 --- a/target/nextflow/gtf2bed/main.nf +++ b/target/nextflow/gtf2bed/main.nf @@ -2995,8 +2995,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gtf2bed", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/gtf_filter/.config.vsh.yaml b/target/nextflow/gtf_filter/.config.vsh.yaml index 2781b12..113b058 100644 --- a/target/nextflow/gtf_filter/.config.vsh.yaml +++ b/target/nextflow/gtf_filter/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/nextflow/gtf_filter" executable: "target/nextflow/gtf_filter/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/gtf_filter/main.nf b/target/nextflow/gtf_filter/main.nf index e81103b..63d5563 100644 --- a/target/nextflow/gtf_filter/main.nf +++ b/target/nextflow/gtf_filter/main.nf @@ -3003,8 +3003,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gtf_filter", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/gunzip/.config.vsh.yaml b/target/nextflow/gunzip/.config.vsh.yaml index f6e4e05..59db67d 100644 --- a/target/nextflow/gunzip/.config.vsh.yaml +++ b/target/nextflow/gunzip/.config.vsh.yaml @@ -144,8 +144,8 @@ build_info: output: "target/nextflow/gunzip" executable: "target/nextflow/gunzip/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/gunzip/main.nf b/target/nextflow/gunzip/main.nf index 5df83af..d59231c 100644 --- a/target/nextflow/gunzip/main.nf +++ b/target/nextflow/gunzip/main.nf @@ -2992,8 +2992,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gunzip", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml index e34fbac..b8b1ccd 100644 --- a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/nextflow/kallisto/kallisto_index" executable: "target/nextflow/kallisto/kallisto_index/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/kallisto/kallisto_index/main.nf b/target/nextflow/kallisto/kallisto_index/main.nf index 12b1beb..933fc2d 100644 --- a/target/nextflow/kallisto/kallisto_index/main.nf +++ b/target/nextflow/kallisto/kallisto_index/main.nf @@ -3002,8 +3002,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_index", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml index cd18fa2..fc9afb7 100644 --- a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/nextflow/kallisto/kallisto_quant" executable: "target/nextflow/kallisto/kallisto_quant/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/kallisto/kallisto_quant/main.nf b/target/nextflow/kallisto/kallisto_quant/main.nf index 21a3774..fa52ad5 100644 --- a/target/nextflow/kallisto/kallisto_quant/main.nf +++ b/target/nextflow/kallisto/kallisto_quant/main.nf @@ -3114,8 +3114,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_quant", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml index a3583fb..646d1b2 100644 --- a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml @@ -170,8 +170,8 @@ build_info: output: "target/nextflow/multiqc_custom_biotype" executable: "target/nextflow/multiqc_custom_biotype/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/multiqc_custom_biotype/main.nf b/target/nextflow/multiqc_custom_biotype/main.nf index 145c950..531d2b2 100644 --- a/target/nextflow/multiqc_custom_biotype/main.nf +++ b/target/nextflow/multiqc_custom_biotype/main.nf @@ -3020,8 +3020,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/multiqc_custom_biotype", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/picard_markduplicates/.config.vsh.yaml b/target/nextflow/picard_markduplicates/.config.vsh.yaml index cf1a1e9..a6b7669 100644 --- a/target/nextflow/picard_markduplicates/.config.vsh.yaml +++ b/target/nextflow/picard_markduplicates/.config.vsh.yaml @@ -207,8 +207,8 @@ build_info: output: "target/nextflow/picard_markduplicates" executable: "target/nextflow/picard_markduplicates/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/picard_markduplicates/main.nf b/target/nextflow/picard_markduplicates/main.nf index a7c7b85..c13504f 100644 --- a/target/nextflow/picard_markduplicates/main.nf +++ b/target/nextflow/picard_markduplicates/main.nf @@ -3063,8 +3063,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/picard_markduplicates", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/prepare_multiqc_input/.config.vsh.yaml b/target/nextflow/prepare_multiqc_input/.config.vsh.yaml index 5cf843f..80635de 100644 --- a/target/nextflow/prepare_multiqc_input/.config.vsh.yaml +++ b/target/nextflow/prepare_multiqc_input/.config.vsh.yaml @@ -409,8 +409,8 @@ build_info: output: "target/nextflow/prepare_multiqc_input" executable: "target/nextflow/prepare_multiqc_input/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/prepare_multiqc_input/main.nf b/target/nextflow/prepare_multiqc_input/main.nf index 8b11a9c..70e06c5 100644 --- a/target/nextflow/prepare_multiqc_input/main.nf +++ b/target/nextflow/prepare_multiqc_input/main.nf @@ -3277,8 +3277,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/prepare_multiqc_input", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml b/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml index bfed330..ad1bec4 100644 --- a/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml +++ b/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml @@ -138,8 +138,8 @@ build_info: output: "target/nextflow/preprocess_transcripts_fasta" executable: "target/nextflow/preprocess_transcripts_fasta/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/preprocess_transcripts_fasta/main.nf b/target/nextflow/preprocess_transcripts_fasta/main.nf index 80d0cf3..30fab61 100644 --- a/target/nextflow/preprocess_transcripts_fasta/main.nf +++ b/target/nextflow/preprocess_transcripts_fasta/main.nf @@ -2982,8 +2982,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/preprocess_transcripts_fasta", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/preseq_lcextrap/.config.vsh.yaml b/target/nextflow/preseq_lcextrap/.config.vsh.yaml index 57dced0..5a9e351 100644 --- a/target/nextflow/preseq_lcextrap/.config.vsh.yaml +++ b/target/nextflow/preseq_lcextrap/.config.vsh.yaml @@ -191,8 +191,8 @@ build_info: output: "target/nextflow/preseq_lcextrap" executable: "target/nextflow/preseq_lcextrap/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/preseq_lcextrap/main.nf b/target/nextflow/preseq_lcextrap/main.nf index 6d38f26..3d836b4 100644 --- a/target/nextflow/preseq_lcextrap/main.nf +++ b/target/nextflow/preseq_lcextrap/main.nf @@ -3035,8 +3035,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/preseq_lcextrap", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/qualimap/.config.vsh.yaml b/target/nextflow/qualimap/.config.vsh.yaml index 362375b..e9aa2d9 100644 --- a/target/nextflow/qualimap/.config.vsh.yaml +++ b/target/nextflow/qualimap/.config.vsh.yaml @@ -271,8 +271,8 @@ build_info: output: "target/nextflow/qualimap" executable: "target/nextflow/qualimap/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/qualimap/main.nf b/target/nextflow/qualimap/main.nf index c431871..70d9a94 100644 --- a/target/nextflow/qualimap/main.nf +++ b/target/nextflow/qualimap/main.nf @@ -3144,8 +3144,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/qualimap", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml index f0fb4c6..b8051e8 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -299,8 +299,8 @@ build_info: output: "target/nextflow/rsem/rsem_calculate_expression" executable: "target/nextflow/rsem/rsem_calculate_expression/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rsem/rsem_calculate_expression/main.nf b/target/nextflow/rsem/rsem_calculate_expression/main.nf index 9369ed7..937b0b3 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/main.nf +++ b/target/nextflow/rsem/rsem_calculate_expression/main.nf @@ -3163,8 +3163,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_calculate_expression", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml b/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml index bb7beb9..7e50f79 100644 --- a/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml @@ -202,8 +202,8 @@ build_info: output: "target/nextflow/rsem/rsem_merge_counts" executable: "target/nextflow/rsem/rsem_merge_counts/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rsem/rsem_merge_counts/main.nf b/target/nextflow/rsem/rsem_merge_counts/main.nf index 83088b4..694751b 100644 --- a/target/nextflow/rsem/rsem_merge_counts/main.nf +++ b/target/nextflow/rsem/rsem_merge_counts/main.nf @@ -3051,8 +3051,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_merge_counts", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml index a64fe6a..2123cd6 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -163,8 +163,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_bamstat" executable: "target/nextflow/rseqc/rseqc_bamstat/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_bamstat/main.nf b/target/nextflow/rseqc/rseqc_bamstat/main.nf index 0d9b3a0..73fdf7b 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/main.nf +++ b/target/nextflow/rseqc/rseqc_bamstat/main.nf @@ -3016,8 +3016,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_bamstat", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml index 9970fd5..90981c8 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -186,8 +186,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_inferexperiment" executable: "target/nextflow/rseqc/rseqc_inferexperiment/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf index e4b2417..cb51c3d 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf +++ b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf @@ -3044,8 +3044,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_inferexperiment", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml index d3c9fa2..c015ee7 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml @@ -272,8 +272,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_innerdistance" executable: "target/nextflow/rseqc/rseqc_innerdistance/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_innerdistance/main.nf b/target/nextflow/rseqc/rseqc_innerdistance/main.nf index 6be7934..c011e35 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/main.nf +++ b/target/nextflow/rseqc/rseqc_innerdistance/main.nf @@ -3137,8 +3137,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_innerdistance", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml index 450b5e5..1352c8d 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml @@ -260,8 +260,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_junctionannotation" executable: "target/nextflow/rseqc/rseqc_junctionannotation/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf index e9f8579..74bf5b4 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf +++ b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf @@ -3128,8 +3128,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionannotation", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index 0d8ae4a..6326d3e 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml @@ -249,8 +249,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_junctionsaturation" executable: "target/nextflow/rseqc/rseqc_junctionsaturation/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf index 5c69d21..21c1861 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf @@ -3113,8 +3113,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionsaturation", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml index 60b4df7..b072903 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml @@ -162,8 +162,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_readdistribution" executable: "target/nextflow/rseqc/rseqc_readdistribution/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_readdistribution/main.nf b/target/nextflow/rseqc/rseqc_readdistribution/main.nf index d05e1ef..677101f 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/main.nf +++ b/target/nextflow/rseqc/rseqc_readdistribution/main.nf @@ -3017,8 +3017,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readdistribution", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml index a9bdd06..88027b3 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml @@ -211,8 +211,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_readduplication" executable: "target/nextflow/rseqc/rseqc_readduplication/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_readduplication/main.nf b/target/nextflow/rseqc/rseqc_readduplication/main.nf index 73dc722..67c9342 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/main.nf +++ b/target/nextflow/rseqc/rseqc_readduplication/main.nf @@ -3071,8 +3071,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readduplication", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml index 703bd5f..9bc3c8f 100644 --- a/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml @@ -214,8 +214,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_tin" executable: "target/nextflow/rseqc/rseqc_tin/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_tin/main.nf b/target/nextflow/rseqc/rseqc_tin/main.nf index 3c29e32..1fe61d1 100644 --- a/target/nextflow/rseqc/rseqc_tin/main.nf +++ b/target/nextflow/rseqc/rseqc_tin/main.nf @@ -3076,8 +3076,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_tin", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/sortmerna/.config.vsh.yaml b/target/nextflow/sortmerna/.config.vsh.yaml index 08d24ec..7816db4 100644 --- a/target/nextflow/sortmerna/.config.vsh.yaml +++ b/target/nextflow/sortmerna/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/nextflow/sortmerna" executable: "target/nextflow/sortmerna/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/sortmerna/main.nf b/target/nextflow/sortmerna/main.nf index 4f44152..eb2a56c 100644 --- a/target/nextflow/sortmerna/main.nf +++ b/target/nextflow/sortmerna/main.nf @@ -3050,8 +3050,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/sortmerna", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/stringtie/.config.vsh.yaml b/target/nextflow/stringtie/.config.vsh.yaml index 5f48e1b..b5df07e 100644 --- a/target/nextflow/stringtie/.config.vsh.yaml +++ b/target/nextflow/stringtie/.config.vsh.yaml @@ -216,8 +216,8 @@ build_info: output: "target/nextflow/stringtie" executable: "target/nextflow/stringtie/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/stringtie/main.nf b/target/nextflow/stringtie/main.nf index 5cae321..fcf8516 100644 --- a/target/nextflow/stringtie/main.nf +++ b/target/nextflow/stringtie/main.nf @@ -3073,8 +3073,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/stringtie", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/summarizedexperiment/.config.vsh.yaml b/target/nextflow/summarizedexperiment/.config.vsh.yaml index c0eb44d..88a8a32 100644 --- a/target/nextflow/summarizedexperiment/.config.vsh.yaml +++ b/target/nextflow/summarizedexperiment/.config.vsh.yaml @@ -199,8 +199,8 @@ build_info: output: "target/nextflow/summarizedexperiment" executable: "target/nextflow/summarizedexperiment/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/summarizedexperiment/main.nf b/target/nextflow/summarizedexperiment/main.nf index 6e7a333..fe31fc2 100644 --- a/target/nextflow/summarizedexperiment/main.nf +++ b/target/nextflow/summarizedexperiment/main.nf @@ -3054,8 +3054,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/summarizedexperiment", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/trimgalore/.config.vsh.yaml b/target/nextflow/trimgalore/.config.vsh.yaml index b584d72..7896ea9 100644 --- a/target/nextflow/trimgalore/.config.vsh.yaml +++ b/target/nextflow/trimgalore/.config.vsh.yaml @@ -788,8 +788,8 @@ build_info: output: "target/nextflow/trimgalore" executable: "target/nextflow/trimgalore/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/trimgalore/main.nf b/target/nextflow/trimgalore/main.nf index b252008..196462b 100644 --- a/target/nextflow/trimgalore/main.nf +++ b/target/nextflow/trimgalore/main.nf @@ -3576,8 +3576,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/trimgalore", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/tx2gene/.config.vsh.yaml b/target/nextflow/tx2gene/.config.vsh.yaml index 02786d6..bb4f2bb 100644 --- a/target/nextflow/tx2gene/.config.vsh.yaml +++ b/target/nextflow/tx2gene/.config.vsh.yaml @@ -192,8 +192,8 @@ build_info: output: "target/nextflow/tx2gene" executable: "target/nextflow/tx2gene/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/tx2gene/main.nf b/target/nextflow/tx2gene/main.nf index 40a639e..149dfc4 100644 --- a/target/nextflow/tx2gene/main.nf +++ b/target/nextflow/tx2gene/main.nf @@ -3049,8 +3049,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tx2gene", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/tximport/.config.vsh.yaml b/target/nextflow/tximport/.config.vsh.yaml index 297ce82..06b69c6 100644 --- a/target/nextflow/tximport/.config.vsh.yaml +++ b/target/nextflow/tximport/.config.vsh.yaml @@ -247,8 +247,8 @@ build_info: output: "target/nextflow/tximport" executable: "target/nextflow/tximport/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/tximport/main.nf b/target/nextflow/tximport/main.nf index 40c3bfe..4b05480 100644 --- a/target/nextflow/tximport/main.nf +++ b/target/nextflow/tximport/main.nf @@ -3114,8 +3114,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tximport", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/ucsc/bedclip/.config.vsh.yaml b/target/nextflow/ucsc/bedclip/.config.vsh.yaml index 02e6920..4c5a513 100644 --- a/target/nextflow/ucsc/bedclip/.config.vsh.yaml +++ b/target/nextflow/ucsc/bedclip/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/nextflow/ucsc/bedclip" executable: "target/nextflow/ucsc/bedclip/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/ucsc/bedclip/main.nf b/target/nextflow/ucsc/bedclip/main.nf index a38427e..3b2c339 100644 --- a/target/nextflow/ucsc/bedclip/main.nf +++ b/target/nextflow/ucsc/bedclip/main.nf @@ -3018,8 +3018,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/ucsc/bedclip", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml index 6c34b26..932f591 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml +++ b/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/nextflow/ucsc/bedgraphtobigwig" executable: "target/nextflow/ucsc/bedgraphtobigwig/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/ucsc/bedgraphtobigwig/main.nf b/target/nextflow/ucsc/bedgraphtobigwig/main.nf index 9622953..0514555 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/main.nf +++ b/target/nextflow/ucsc/bedgraphtobigwig/main.nf @@ -3018,8 +3018,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/ucsc/bedgraphtobigwig", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml b/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml index 2a25145..5f6530e 100644 --- a/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml +++ b/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml @@ -195,8 +195,8 @@ build_info: output: "target/nextflow/umitools/umitools_dedup" executable: "target/nextflow/umitools/umitools_dedup/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/umitools/umitools_dedup/main.nf b/target/nextflow/umitools/umitools_dedup/main.nf index a892679..36f5f3f 100644 --- a/target/nextflow/umitools/umitools_dedup/main.nf +++ b/target/nextflow/umitools/umitools_dedup/main.nf @@ -3054,8 +3054,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_dedup", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/umitools/umitools_extract/.config.vsh.yaml b/target/nextflow/umitools/umitools_extract/.config.vsh.yaml index edec974..d4057dd 100644 --- a/target/nextflow/umitools/umitools_extract/.config.vsh.yaml +++ b/target/nextflow/umitools/umitools_extract/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/nextflow/umitools/umitools_extract" executable: "target/nextflow/umitools/umitools_extract/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/umitools/umitools_extract/main.nf b/target/nextflow/umitools/umitools_extract/main.nf index c9dee76..5c24ff0 100644 --- a/target/nextflow/umitools/umitools_extract/main.nf +++ b/target/nextflow/umitools/umitools_extract/main.nf @@ -3119,8 +3119,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_extract", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/umitools_prepareforquant/.config.vsh.yaml b/target/nextflow/umitools_prepareforquant/.config.vsh.yaml index 826a79e..48979d0 100644 --- a/target/nextflow/umitools_prepareforquant/.config.vsh.yaml +++ b/target/nextflow/umitools_prepareforquant/.config.vsh.yaml @@ -156,8 +156,8 @@ build_info: output: "target/nextflow/umitools_prepareforquant" executable: "target/nextflow/umitools_prepareforquant/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/umitools_prepareforquant/main.nf b/target/nextflow/umitools_prepareforquant/main.nf index a745c17..b16e62e 100644 --- a/target/nextflow/umitools_prepareforquant/main.nf +++ b/target/nextflow/umitools_prepareforquant/main.nf @@ -3007,8 +3007,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools_prepareforquant", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml b/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml index f88f7e8..e401a6d 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -596,8 +596,8 @@ build_info: output: "target/nextflow/workflows/genome_alignment_and_quant" executable: "target/nextflow/workflows/genome_alignment_and_quant/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" diff --git a/target/nextflow/workflows/genome_alignment_and_quant/main.nf b/target/nextflow/workflows/genome_alignment_and_quant/main.nf index 24edb7d..6019532 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/genome_alignment_and_quant/main.nf @@ -3523,8 +3523,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/genome_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml b/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml index 7d36b8a..762253e 100644 --- a/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml +++ b/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml @@ -278,8 +278,8 @@ build_info: output: "target/nextflow/workflows/merge_quant_results" executable: "target/nextflow/workflows/merge_quant_results/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/tx2gene" - "target/nextflow/tximport" diff --git a/target/nextflow/workflows/merge_quant_results/main.nf b/target/nextflow/workflows/merge_quant_results/main.nf index a3af60e..33d7f1b 100644 --- a/target/nextflow/workflows/merge_quant_results/main.nf +++ b/target/nextflow/workflows/merge_quant_results/main.nf @@ -3149,8 +3149,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/merge_quant_results", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/post_processing/.config.vsh.yaml b/target/nextflow/workflows/post_processing/.config.vsh.yaml index 49c2658..909bfa0 100644 --- a/target/nextflow/workflows/post_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/post_processing/.config.vsh.yaml @@ -486,8 +486,8 @@ build_info: output: "target/nextflow/workflows/post_processing" executable: "target/nextflow/workflows/post_processing/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" diff --git a/target/nextflow/workflows/post_processing/main.nf b/target/nextflow/workflows/post_processing/main.nf index 9d5840a..8554465 100644 --- a/target/nextflow/workflows/post_processing/main.nf +++ b/target/nextflow/workflows/post_processing/main.nf @@ -3397,8 +3397,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/post_processing", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/pre_processing/.config.vsh.yaml b/target/nextflow/workflows/pre_processing/.config.vsh.yaml index 29edd00..01f0991 100644 --- a/target/nextflow/workflows/pre_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/pre_processing/.config.vsh.yaml @@ -510,6 +510,40 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" + - type: "file" + name: "--trim_json" + description: "The fastp json format report file name" + info: null + default: + - "$id.fastp_out.json" + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--trim_html" + description: "The fastp html format report file name" + info: null + default: + - "$id.fastp_out.html" + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" + - type: "file" + name: "--merged_out" + description: "File name to store merged fastp output." + info: null + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" resources: - type: "nextflow_script" path: "main.nf" @@ -639,8 +673,8 @@ build_info: output: "target/nextflow/workflows/pre_processing" executable: "target/nextflow/workflows/pre_processing/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/fastqc" - "target/nextflow/umitools/umitools_extract" diff --git a/target/nextflow/workflows/pre_processing/main.nf b/target/nextflow/workflows/pre_processing/main.nf index 3f1d0a3..a149601 100644 --- a/target/nextflow/workflows/pre_processing/main.nf +++ b/target/nextflow/workflows/pre_processing/main.nf @@ -3406,6 +3406,45 @@ meta = [ "direction" : "output", "multiple" : false, "multiple_sep" : ";" + }, + { + "type" : "file", + "name" : "--trim_json", + "description" : "The fastp json format report file name", + "default" : [ + "$id.fastp_out.json" + ], + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "output", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "file", + "name" : "--trim_html", + "description" : "The fastp html format report file name", + "default" : [ + "$id.fastp_out.html" + ], + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "output", + "multiple" : false, + "multiple_sep" : ";" + }, + { + "type" : "file", + "name" : "--merged_out", + "description" : "File name to store merged fastp output.", + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "output", + "multiple" : false, + "multiple_sep" : ";" } ] } @@ -3587,8 +3626,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pre_processing", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/pre_processing/nextflow_schema.json b/target/nextflow/workflows/pre_processing/nextflow_schema.json index ee5344d..1b49356 100644 --- a/target/nextflow/workflows/pre_processing/nextflow_schema.json +++ b/target/nextflow/workflows/pre_processing/nextflow_schema.json @@ -584,6 +584,39 @@ } + , + "trim_json": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.trim_json.json`. The fastp json format report file name", + "help_text": "Type: `file`, default: `$id.$key.trim_json.json`. The fastp json format report file name" + , + "default": "$id.$key.trim_json.json" + } + + + , + "trim_html": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.trim_html.html`. The fastp html format report file name", + "help_text": "Type: `file`, default: `$id.$key.trim_html.html`. The fastp html format report file name" + , + "default": "$id.$key.trim_html.html" + } + + + , + "merged_out": { + "type": + "string", + "description": "Type: `file`, default: `$id.$key.merged_out.merged_out`. File name to store merged fastp output", + "help_text": "Type: `file`, default: `$id.$key.merged_out.merged_out`. File name to store merged fastp output." + , + "default": "$id.$key.merged_out.merged_out" + } + + } }, diff --git a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml index 9952825..9d11a81 100644 --- a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml +++ b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml @@ -496,8 +496,8 @@ build_info: output: "target/nextflow/workflows/prepare_genome" executable: "target/nextflow/workflows/prepare_genome/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread" diff --git a/target/nextflow/workflows/prepare_genome/main.nf b/target/nextflow/workflows/prepare_genome/main.nf index 70e37a2..22c8b66 100644 --- a/target/nextflow/workflows/prepare_genome/main.nf +++ b/target/nextflow/workflows/prepare_genome/main.nf @@ -3407,8 +3407,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/prepare_genome", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml b/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml index 02aca11..53dd648 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -285,8 +285,8 @@ build_info: output: "target/nextflow/workflows/pseudo_alignment_and_quant" executable: "target/nextflow/workflows/pseudo_alignment_and_quant/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" - "target/nextflow/kallisto/kallisto_quant" diff --git a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf index 47dfcd6..bfdc993 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf @@ -3146,8 +3146,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pseudo_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/quality_control/.config.vsh.yaml b/target/nextflow/workflows/quality_control/.config.vsh.yaml index e0e62e7..de45c94 100644 --- a/target/nextflow/workflows/quality_control/.config.vsh.yaml +++ b/target/nextflow/workflows/quality_control/.config.vsh.yaml @@ -1367,7 +1367,7 @@ argument_groups: name: "--pseudo_tpm_gene" info: null default: - - "salmon.merged.pseudo_gene_tpm.tsv" + - "pseudo_gene_tpm.tsv" must_exist: true create_parent: true required: false @@ -1378,7 +1378,7 @@ argument_groups: name: "--pseudo_counts_gene" info: null default: - - "salmon.merged.pseudo_gene_counts.tsv" + - "pseudo_gene_counts.tsv" must_exist: true create_parent: true required: false @@ -1389,7 +1389,7 @@ argument_groups: name: "--pseudo_counts_gene_length_scaled" info: null default: - - "salmon.merged.pseudo_gene_counts_length_scaled.tsv" + - "pseudo_gene_counts_length_scaled.tsv" must_exist: true create_parent: true required: false @@ -1400,7 +1400,7 @@ argument_groups: name: "--pseudo_counts_gene_scaled" info: null default: - - "salmon.merged.pseudo_gene_counts_scaled.tsv" + - "pseudo_gene_counts_scaled.tsv" must_exist: true create_parent: true required: false @@ -1411,7 +1411,7 @@ argument_groups: name: "--pseudo_tpm_transcript" info: null default: - - "salmon.merged.pseudo_transcript_tpm.tsv" + - "pseudo_transcript_tpm.tsv" must_exist: true create_parent: true required: false @@ -1422,7 +1422,7 @@ argument_groups: name: "--pseudo_counts_transcript" info: null default: - - "salmon.merged.pseudo_transcript_counts.tsv" + - "pseudo_transcript_counts.tsv" must_exist: true create_parent: true required: false @@ -1592,8 +1592,8 @@ build_info: output: "target/nextflow/workflows/quality_control" executable: "target/nextflow/workflows/quality_control/main.nf" viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5" + git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/rseqc/rseqc_bamstat" - "target/nextflow/rseqc/rseqc_inferexperiment" diff --git a/target/nextflow/workflows/quality_control/main.nf b/target/nextflow/workflows/quality_control/main.nf index 2b8be5c..b484e35 100644 --- a/target/nextflow/workflows/quality_control/main.nf +++ b/target/nextflow/workflows/quality_control/main.nf @@ -4356,7 +4356,7 @@ meta = [ "type" : "file", "name" : "--pseudo_tpm_gene", "default" : [ - "salmon.merged.pseudo_gene_tpm.tsv" + "pseudo_gene_tpm.tsv" ], "must_exist" : true, "create_parent" : true, @@ -4369,7 +4369,7 @@ meta = [ "type" : "file", "name" : "--pseudo_counts_gene", "default" : [ - "salmon.merged.pseudo_gene_counts.tsv" + "pseudo_gene_counts.tsv" ], "must_exist" : true, "create_parent" : true, @@ -4382,7 +4382,7 @@ meta = [ "type" : "file", "name" : "--pseudo_counts_gene_length_scaled", "default" : [ - "salmon.merged.pseudo_gene_counts_length_scaled.tsv" + "pseudo_gene_counts_length_scaled.tsv" ], "must_exist" : true, "create_parent" : true, @@ -4395,7 +4395,7 @@ meta = [ "type" : "file", "name" : "--pseudo_counts_gene_scaled", "default" : [ - "salmon.merged.pseudo_gene_counts_scaled.tsv" + "pseudo_gene_counts_scaled.tsv" ], "must_exist" : true, "create_parent" : true, @@ -4408,7 +4408,7 @@ meta = [ "type" : "file", "name" : "--pseudo_tpm_transcript", "default" : [ - "salmon.merged.pseudo_transcript_tpm.tsv" + "pseudo_transcript_tpm.tsv" ], "must_exist" : true, "create_parent" : true, @@ -4421,7 +4421,7 @@ meta = [ "type" : "file", "name" : "--pseudo_counts_transcript", "default" : [ - "salmon.merged.pseudo_transcript_counts.tsv" + "pseudo_transcript_counts.tsv" ], "must_exist" : true, "create_parent" : true, @@ -4669,8 +4669,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/quality_control", "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" + "git_commit" : "de0a35359a44844ab9f5f99a38a4d13a457b05a5", + "git_remote" : "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/rnaseq/.config.vsh.yaml b/target/nextflow/workflows/rnaseq/.config.vsh.yaml deleted file mode 100644 index 7c5434a..0000000 --- a/target/nextflow/workflows/rnaseq/.config.vsh.yaml +++ /dev/null @@ -1,1991 +0,0 @@ -name: "rnaseq" -namespace: "workflows" -version: "multiple_fixes" -argument_groups: -- name: "Input" - arguments: - - type: "string" - name: "--id" - description: "ID of the sample." - info: null - example: - - "foo" - required: true - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--fastq_1" - description: "Path to the sample (or read 1 of paired end sample)." - info: null - must_exist: true - create_parent: true - required: true - direction: "input" - multiple: true - multiple_sep: ";" - - type: "file" - name: "--fastq_2" - description: "Path to read 2 of the sample." - info: null - must_exist: false - create_parent: true - required: false - direction: "input" - multiple: true - multiple_sep: ";" - - type: "string" - name: "--strandedness" - description: "Sample strand-specificity. Must be one of unstranded, forward, reverse\ - \ or auto" - info: null - default: - - "auto" - required: false - choices: - - "unstranded" - - "forward" - - "reverse" - - "auto" - direction: "input" - multiple: false - multiple_sep: ";" -- name: "Reference genome options" - arguments: - - type: "file" - name: "--fasta" - description: "Path to FASTA genome file." - info: null - must_exist: true - create_parent: true - required: true - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--gtf" - description: "Path to GTF annotation file. This parameter is *mandatory* if --genome\ - \ is not specified." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--gff" - description: "Path to GFF3 annotation file. Required if \"--gtf\" is not specified." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--additional_fasta" - description: "FASTA file to concatenate to genome FASTA file e.g. containing spike-in\ - \ sequences." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--transcript_fasta" - description: "Path to FASTA transcriptome file." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--gene_bed" - description: "Path to BED file containing gene intervals. This will be created\ - \ from the GTF file if not specified." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--splicesites" - description: "Splice sites file required for HISAT2." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--star_index" - description: "Path to directory or tar.gz archive for pre-built STAR index." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--rsem_index" - description: "Path to directory or tar.gz archive for pre-built RSEM index." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--salmon_index" - description: "Path to directory or tar.gz archive for pre-built Salmon index." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--kallisto_index" - description: "Path to directory or tar.gz archive for pre-built Kallisto index." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean_true" - name: "--gencode" - description: "Specify if the GTF annotation is in GENCODE format." - info: null - direction: "input" - - type: "string" - name: "--gtf_extra_attributes" - description: "Additional gene identifiers from the input GTF file when running\ - \ Salmon. More than one value can be specified separated by comma." - info: null - default: - - "gene_name" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--gtf_group_features" - description: "Define the attribute type used to group features in the GTF file\ - \ when running Salmon." - info: null - default: - - "gene_id" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--featurecounts_group_type" - description: "The attribute type used to group feature types in the GTF file when\ - \ generating the biotype plot with featureCounts." - info: null - default: - - "gene_biotype" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--featurecounts_feature_type" - description: "By default, the pipeline assigns reads based on the 'exon' attribute\ - \ within the GTF file." - info: null - default: - - "exon" - required: false - direction: "input" - multiple: false - multiple_sep: ";" -- name: "Read trimming options" - arguments: - - type: "string" - name: "--trimmer" - description: "Specify the trimming tool to use." - info: null - default: - - "trimgalore" - required: false - choices: - - "trimgalore" - - "fastp" - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--extra_trimgalore_args" - description: "Extra arguments to pass to Trim Galore! command in addition to defaults\ - \ defined by the pipeline." - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--extra_fastp_args" - description: "Extra arguments to pass to fastp command in addition to defaults\ - \ defined by the pipeline." - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "integer" - name: "--min_trimmed_reads" - description: "Minimum number of trimmed reads below which samples are removed\ - \ from further processing. Some downstream steps in the pipeline will fail if\ - \ this threshold is too low." - info: null - default: - - 10000 - required: false - direction: "input" - multiple: false - multiple_sep: ";" -- name: "Read filtering options" - arguments: - - type: "file" - name: "--bbsplit_fasta_list" - description: "Path to comma-separated file containing a list of reference genomes\ - \ to filter reads against with BBSplit. To use BBSplit, \"--skip_bbsplit\" must\ - \ be explicitly set to \"false\". The file should contain 2 (comma separated)\ - \ columns - short name and full path to reference genome(s)" - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--bbsplit_index" - description: "Path to directory or tar.gz archive for pre-built BBSplit index." - info: null - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean_true" - name: "--remove_ribo_rna" - description: "Enable the removal of reads derived from ribosomal RNA using SortMeRNA." - info: null - direction: "input" - - type: "file" - name: "--ribo_database_manifest" - description: "Text file containing paths to fasta files (one per line) that will\ - \ be used to create the database for SortMeRNA." - info: null - default: - - "assets/rrna-db-defaults.txt" - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" -- name: "UMI options" - arguments: - - type: "boolean_true" - name: "--with_umi" - description: "Enable UMI-based read deduplication." - info: null - direction: "input" - - type: "string" - name: "--umitools_extract_method" - description: "UMI pattern to use." - info: null - default: - - "string" - required: false - choices: - - "string" - - "regex" - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--umitools_bc_pattern" - description: "The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the\ - \ first 6 nucleotides of the read are from the UMI." - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--umitools_bc_pattern2" - description: "The UMI barcode pattern to use if the UMI is located in read 2." - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "integer" - name: "--umi_discard_read" - description: "After UMI barcode extraction discard either R1 or R2 by setting\ - \ this parameter to 1 or 2, respectively." - info: null - default: - - 0 - required: false - choices: - - 0 - - 1 - - 2 - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--umitools_umi_separator" - description: "The character that separates the UMI in the read name. Most likely\ - \ a colon if you skipped the extraction with UMI-tools and used other software." - info: null - default: - - "_" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--umitools_grouping_method" - description: "Method to use to determine read groups by subsuming those with similar\ - \ UMIs. All methods start by identifying the reads with the same mapping position,\ - \ but treat similar yet nonidentical UMIs differently." - info: null - default: - - "directional" - required: false - choices: - - "unique" - - "percentile" - - "cluster" - - "adjacency" - - "directional" - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean_true" - name: "--umi_dedup_stats" - description: "Generate output stats when running \"umi_tools dedup\"." - info: null - direction: "input" -- name: "Alignment options" - arguments: - - type: "string" - name: "--aligner" - description: "Specifies the alignment algorithm to use - available options are\ - \ 'star_salmon', 'star_rsem' and 'hisat2'." - info: null - default: - - "star_salmon" - required: false - choices: - - "star_salmon" - - "star_rsem" - - "hisat2" - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--pseudo_aligner" - description: "Specifies the pseudo aligner to use - available options are 'salmon'.\ - \ Runs in addition to '--aligner'." - info: null - default: - - "salmon" - required: false - choices: - - "salmon" - - "kallisto" - direction: "input" - multiple: false - multiple_sep: ";" - - type: "integer" - name: "--pseudo_aligner_kmer_size" - description: "Kmer length passed to indexing step of pseudoaligners." - info: null - default: - - 31 - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "integer" - name: "--kallisto_quant_fragment_length" - description: "For single-end mode only, the estimated average fragment length\ - \ to use for quantification with Kallisto." - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "integer" - name: "--kallisto_quant_fragment_length_sd" - description: "For single-end mode only, the estimated standard deviation of the\ - \ fragment length for quantification with Kallisto." - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean_true" - name: "--bam_csi_index" - description: "Create a CSI index for BAM files instead of the traditional BAI\ - \ index. This will be required for genomes with larger chromosome sizes." - info: null - direction: "input" - - type: "string" - name: "--salmon_quant_libtype" - description: "Override Salmon library type inferred based on strandedness defined\ - \ in meta object." - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--extra_salmon_quant_args" - description: "Extra arguments to pass to salmon quant command in addition to defaults\ - \ defined by the pipeline." - info: null - default: - - "-v" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "integer" - name: "--min_mapped_reads" - description: "Minimum percentage of uniquely mapped reads below which samples\ - \ are removed from further processing." - info: null - default: - - 5 - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean_true" - name: "--stringtie_ignore_gtf" - description: "Perform reference-guided de novo assembly of transcripts using StringTie,\ - \ i.e. don't restrict to those in GTF file." - info: null - direction: "input" - - type: "string" - name: "--extra_stringtie_args" - description: "Extra arguments to pass to stringtie command in addition to defaults\ - \ defined by the pipeline." - info: null - default: - - "-v" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean_true" - name: "--save_unaligned" - description: "Where possible, save unaligned reads from either STAR, HISAT2 or\ - \ Salmon to the results directory." - info: null - direction: "input" - - type: "boolean_true" - name: "--save_align_intermeds" - description: "Save the intermediate BAM files from the alignment step." - info: null - direction: "input" - - type: "boolean_true" - name: "--skip_alignment" - description: "Skip all of the alignment-based processes within the pipeline." - info: null - direction: "input" - - type: "boolean_true" - name: "--skip_pseudo_alignment" - description: "Skip all of the pseudo-alignment-based processes within the pipeline." - info: null - direction: "input" - - type: "string" - name: "--extra_rsem_calculate_expression_args" - description: "Extra arguments to pass to rsem-calculate-expression command in\ - \ addition to defaults defined by the pipeline." - info: null - default: - - "--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed\ - \ 1" - required: false - direction: "input" - multiple: false - multiple_sep: ";" -- name: "Process skipping options" - arguments: - - type: "boolean" - name: "--skip_fastqc" - description: "Skip FatQC step." - info: null - default: - - false - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean" - name: "--skip_trimming" - description: "Skip the adapter trimming step." - info: null - default: - - false - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean_true" - name: "--skip_bbsplit" - description: "Skip BBSplit for removal of non-reference genome reads." - info: null - direction: "input" - - type: "boolean" - name: "--skip_umi_extract" - description: "Skip umi_tools extract step." - info: null - default: - - false - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean_true" - name: "--skip_qc" - description: "Skip all QC steps except for MultiQC." - info: null - direction: "input" - - type: "boolean_true" - name: "--skip_markduplicates" - description: "Skip picard MarkDuplicates step." - info: null - direction: "input" - - type: "boolean_true" - name: "--skip_stringtie" - description: "Skip StringTie." - info: null - direction: "input" - - type: "boolean_true" - name: "--skip_biotype_qc" - description: "Skip additional featureCounts process for biotype QC." - info: null - direction: "input" - - type: "boolean_true" - name: "--skip_bigwig" - description: "Skip bigWig file creation." - info: null - direction: "input" - - type: "boolean_true" - name: "--skip_preseq" - description: "Skip Preseq." - info: null - direction: "input" - - type: "boolean_true" - name: "--skip_deseq2_qc" - description: "Skip DESeq2 PCA and heatmap plotting." - info: null - direction: "input" - - type: "boolean_true" - name: "skip_dupradar" - description: "Skip dupRadar." - info: null - direction: "input" - - type: "boolean_true" - name: "skip_rseqc" - description: "Skip RSeQC." - info: null - direction: "input" - - type: "boolean_true" - name: "skip_multiqc" - description: "Skip MultiQC." - info: null - direction: "input" -- name: "Other process arguments" - arguments: - - type: "string" - name: "--extra_fq_subsample_args" - description: "Extra arguments to pass to fq subsample command in addition to defaults\ - \ defined by the pipeline." - info: null - default: - - " --record-count 1000000 --seed 1" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--extra_picard_args" - description: "Extra arguments to pass to picard MarkDuplicates command in addition\ - \ to defaults defined by the pipeline." - info: null - default: - - " --ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT\ - \ --TMP_DIR tmp" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--extra_bedtools_args" - description: "Extra arguments to pass to bedtools genomecov command in addition\ - \ to defaults defined by the pipeline." - info: null - default: - - " -split -du" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--extra_featurecounts_args" - description: "Extra arguments to pass to featureCounts command in addition to\ - \ defaults defined by the pipeline" - info: null - default: - - " -B -C" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--extra_preseq_args" - description: "Extra arguments to pass to preseq lc_extrap command in addition\ - \ to defaults defined by the pipeline" - info: null - default: - - "-verbose -seed 1 -seg_len 100000000" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--pca_header_multiqc" - info: null - default: - - "assets/multiqc/deseq2_pca_header.txt" - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--clustering_header_multiqc" - info: null - default: - - "assets/multiqc/deseq2_clustering_header.txt" - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "boolean" - name: "--deseq2_vst" - description: "Use vst transformation instead of rlog with DESeq2" - info: null - default: - - true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--extra_deseq2_args" - info: null - default: - - "--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--extra_deseq2_args2" - info: null - default: - - "star_salmon" - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--rseqc_modules" - description: "Specify the RSeQC modules to run_wf" - info: null - default: - - "bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication" - required: false - choices: - - "bam_stat" - - "inner_distance" - - "infer_experiment" - - "junction_annotation" - - "junction_saturation" - - "read_distribution" - - "read_duplication" - - "tin" - direction: "input" - multiple: true - multiple_sep: "," -- name: "Multiqc paramenters" - arguments: - - type: "file" - name: "--multiqc_custom_config" - info: null - default: - - "assets/multiqc_config.yml" - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "string" - name: "--multiqc_title" - info: null - required: false - direction: "input" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--multiqc_methods_description" - info: null - default: - - "assets/methods_description_template.yml" - must_exist: true - create_parent: true - required: false - direction: "input" - multiple: false - multiple_sep: ";" -- name: "Output" - arguments: - - type: "file" - name: "--output_fasta" - info: null - default: - - "genome/reference_genome.fasta" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--output_gtf" - info: null - default: - - "genome/gene_annotation.gtf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--output_transcript_fasta" - info: null - default: - - "genome/transcriptome.fasta" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--output_gene_bed" - info: null - default: - - "genome/gene_annotation.bed" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--output_star_index" - description: "Path to STAR index." - info: null - default: - - "genome/index/STAR" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--output_salmon_index" - description: "Path to Salmon index." - info: null - default: - - "genome/index/Salmon" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--output_bbsplit_index" - description: "Path to BBSplit index." - info: null - default: - - "genome/index/BBSplit" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--output_kallisto_index" - description: "Path to Kallisto index." - info: null - default: - - "genome/index/Kallisto" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--output_fastq_1" - description: "Path to output directory" - info: null - default: - - "fastq/$id.read_1.fastq" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--output_fastq_2" - description: "Path to output directory" - info: null - default: - - "fastq/$id.read_2.fastq" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--fastqc_html_1" - description: "FastQC HTML report for read 1." - info: null - default: - - "fastqc_raw/$id.read_1.fastqc.html" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--fastqc_html_2" - description: "FastQC HTML report for read 2." - info: null - default: - - "fastqc_raw/$id.read_2.fastqc.html" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--fastqc_zip_1" - description: "FastQC report archive for read 1." - info: null - default: - - "fastqc_raw/$id.read_1.fastqc.zip" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--fastqc_zip_2" - description: "FastQC report archive for read 2." - info: null - default: - - "fastqc_raw/$id.read_2.fastqc.zip" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--trim_log_1" - info: null - default: - - "trimgalore/$id.read_1.trimming_report.txt" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--trim_log_2" - info: null - default: - - "trimgalore/$id.read_2.trimming_report.txt" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--trim_html_1" - info: null - default: - - "fastqc_trim/$id.read_1.trimmed_fastqc.html" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--trim_html_2" - info: null - default: - - "fastqc_trim/$id.read_2.trimmed_fastqc.html" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--trim_zip_1" - info: null - default: - - "fastqc_trim/$id.read_1.trimmed_fastqc.zip" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--trim_zip_2" - info: null - default: - - "fastqc_trim/$id.read_2.trimmed_fastqc.zip" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--sortmerna_log" - description: "Sortmerna log file." - info: null - default: - - "sortmerna/$id.log" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--star_alignment" - info: null - default: - - "STAR_alignment/$id" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--genome_bam_sorted" - info: null - default: - - "STAR_alignment/genome_processed/$id.genome.bam" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--genome_bam_index" - info: null - default: - - "STAR_alignment/genome_processed/$id.genome.bam.bai" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--genome_bam_stats" - info: null - default: - - "samtools_stats/$id.genome.stats" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--genome_bam_flagstat" - info: null - default: - - "samtools_stats/$id.genome.flagstat" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--genome_bam_idxstats" - info: null - default: - - "samtools_stats/$id.genome.idxstats" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--transcriptome_bam" - info: null - default: - - "STAR_alignment/transcriptome_processed/$id.transcriptome.bam" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--transcriptome_bam_index" - info: null - default: - - "STAR_alignment/transcriptome_processed/$id.transcriptome.bam.bai" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--transcriptome_bam_stats" - info: null - default: - - "samtools_stats/$id.transcriptome.stats" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--transcriptome_bam_flagstat" - info: null - default: - - "samtools_stats/$id.transcriptome.flagstat" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--transcriptome_bam_idxstats" - info: null - default: - - "samtools_stats/$id.transcriptome.idxstats" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--salmon_quant_results" - info: null - default: - - "salmon/$id" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--tpm_gene" - info: null - default: - - "salmon/gene_tpm.tsv" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--counts_gene" - info: null - default: - - "salmon/gene_counts.tsv" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--counts_gene_length_scaled" - info: null - default: - - "salmon/gene_counts_length_scaled.tsv" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--counts_gene_scaled" - info: null - default: - - "salmon/gene_counts_scaled.tsv" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--tpm_transcript" - info: null - default: - - "salmon/transcript_tpm.tsv" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--counts_transcript" - info: null - default: - - "salmon/transcript_counts.tsv" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--salmon_merged_summarizedexperiment" - info: null - default: - - "salmon/summarizedexperiment" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--markduplicates_metrics" - info: null - default: - - "picard/$id.sorted.MarkDuplicates.metrics.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--stringtie_transcript_gtf" - info: null - default: - - "stringtie/$id.transcripts.gtf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--stringtie_coverage_gtf" - info: null - default: - - "stringtie/$id.coverage.gtf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--stringtie_abundance" - info: null - default: - - "stringtie/$id.gene_abundance.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--stringtie_ballgown" - info: null - default: - - "stringtie/$id.ballgown" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--featurecounts" - info: null - default: - - "featurecounts/$id.featureCounts.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--featurecounts_summary" - info: null - default: - - "featurecounts/$id.featureCounts.txt.summary" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--featurecounts_multiqc" - info: null - default: - - "featurecounts/$id.featureCounts_mqc.tsv" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--featurecounts_rrna_multiqc" - info: null - default: - - "featurecounts/$id.featureCounts_rrna_mqc.tsv" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--bedgraph_forward" - info: null - default: - - "bedgraph/$id.forward.bedgraph" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--bedgraph_reverse" - info: null - default: - - "bedgraph/$id.reverse.bedgraph" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--bigwig_forward" - info: null - default: - - "bigwig/$id.forward.bigwig" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--bigwig_reverse" - info: null - default: - - "bigwig/$id.reverse.bigwig" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--preseq_output" - info: null - default: - - "preseq/$id.lc_extrap.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--bamstat_output" - description: "Path to output file (txt) of mapping quality statistics" - info: null - default: - - "RSeQC/bamstat/$id.mapping_quality.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--strandedness_output" - description: "Path to output report (txt) of inferred strandedness" - info: null - default: - - "RSeQC/inferexperiment/$id.strandedness.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--inner_dist_output_stats" - description: "output file (txt) with summary statistics of inner distances of\ - \ paired reads" - info: null - default: - - "RSeQC/innerdistance/$id.inner_distance.stats" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--inner_dist_output_dist" - description: "output file (txt) with inner distances of all paired reads" - info: null - default: - - "RSeQC/innerdistance/txt/$id.inner_distance.txt" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--inner_dist_output_freq" - description: "output file (txt) with frequencies of inner distances of all paired\ - \ reads" - info: null - default: - - "RSeQC/innerdistance/txt/$id.inner_distance_freq.txt" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--inner_dist_output_plot" - description: "output file (pdf) with histogram plot of of inner distances of all\ - \ paired reads" - info: null - default: - - "RSeQC/innerdistance/pdf/$id.inner_distance_plot.pdf" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--inner_dist_output_plot_r" - description: "output file (R) with script of histogram plot of of inner distances\ - \ of all paired reads" - info: null - default: - - "RSeQC/innerdistance/rscript/$id.inner_distance_plot.r" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--junction_annotation_output_log" - description: "output log of junction annotation script" - info: null - default: - - "RSeQC/junctionannotation/log/$id.junction_annotation.log" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--junction_annotation_output_plot_r" - description: "R script to generate splice_junction and splice_events plot" - info: null - default: - - "RSeQC/junctionannotation/rscript/$id.junction_annotation_plot.r" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--junction_annotation_output_junction_bed" - description: "junction annotation file (bed format)" - info: null - default: - - "RSeQC/junctionannotation/bed/$id.junction_annotation.bed" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--junction_annotation_output_junction_interact" - description: "interact file (bed format) of junctions. Can be uploaded to UCSC\ - \ genome browser or converted to bigInteract (using bedToBigBed program) for\ - \ visualization." - info: null - default: - - "RSeQC/junctionannotation/bed/$id.junction_annotation.Interact.bed" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--junction_annotation_output_junction_sheet" - description: "junction annotation file (xls format)" - info: null - default: - - "RSeQC/junctionannotation/xls/$id.junction_annotation.xls" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--junction_annotation_output_splice_events_plot" - description: "plot of splice events (pdf)" - info: null - default: - - "RSeQC/junctionannotation/pdf/$id.splice_events.pdf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--junction_annotation_output_splice_junctions_plot" - description: "plot of junctions (pdf)" - info: null - default: - - "RSeQC/junctionannotation/pdf/$id.splice_junctions_plot.pdf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--junction_saturation_output_plot_r" - description: "r script to generate junction_saturation_plot plot" - info: null - default: - - "RSeQC/junctionsaturation/rscript/$id.junction_saturation_plot.r" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--junction_saturation_output_plot" - description: "plot of junction saturation (pdf" - info: null - default: - - "RSeQC/junctionsaturation/pdf/$id.junction_saturation_plot.pdf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--read_distribution_output" - description: "output file (txt) of read distribution analysis." - info: null - default: - - "RSeQC/readdistribution/$id.read_distribution.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--read_duplication_output_duplication_rate_plot_r" - description: "R script for generating duplication rate plot" - info: null - default: - - "RSeQC/readduplication/rscrpt/$id.duplication_rate_plot.r" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--read_duplication_output_duplication_rate_plot" - description: "duplication rate plot (pdf)" - info: null - default: - - "RSeQC/readduplication/pdf/$id.duplication_rate_plot.pdf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--read_duplication_output_duplication_rate_mapping" - description: "Summary of mapping-based read duplication" - info: null - default: - - "RSeQC/readduplication/xls/$id.duplication_rate_mapping.xls" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--read_duplication_output_duplication_rate_sequence" - description: "Summary of sequencing-based read duplication" - info: null - default: - - "RSeQC/readduplication/xls/$id.duplication_rate_sequencing.xls" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--tin_output_summary" - description: "summary statistics (txt) of calculated TIN metrics" - info: null - default: - - "RSeQC/tin/txt/$id.tin_summary.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--tin_output_metrics" - description: "file with TIN metrics (xls)" - info: null - default: - - "RSeQC/tin/xls/$id.tin.xls" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--dupradar_output_dupmatrix" - description: "path to output file (txt) of duplicate tag counts" - info: null - default: - - "dupradar/gene_data/$id.dup_matrix.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--dupradar_output_dup_intercept_mqc" - description: "path to output file (txt) of multiqc intercept value DupRadar" - info: null - default: - - "dupradar/mqc_intercept/$id.dup_intercept_mqc.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--dupradar_output_duprate_exp_boxplot" - description: "path to output file (pdf) of distribution of expression box plot" - info: null - default: - - "dupradar/box_plot/$id.duprate_exp_boxplot.pdf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--dupradar_output_duprate_exp_densplot" - description: "path to output file (pdf) of 2D density scatter plot of duplicate\ - \ tag counts" - info: null - default: - - "dupradar/scatter_plot/$id.duprate_exp_densityplot.pdf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--dupradar_output_duprate_exp_denscurve_mqc" - description: "path to output file (pdf) of density curve of gene duplication multiqc" - info: null - default: - - "dupradar/density_curve/$id.duprate_exp_density_curve_mqc.pdf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--dupradar_output_expression_histogram" - description: "path to output file (pdf) of distribution of RPK values per gene\ - \ histogram" - info: null - default: - - "dupradar/histogram/$id.expression_hist.pdf" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--dupradar_output_intercept_slope" - info: null - default: - - "dupradar/intercept_slope/$id.intercept_slope.txt" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--qualimap_output_pdf" - info: null - default: - - "qualimap/$id.qualimap_output.pdf" - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--qualimap_output_dir" - info: null - default: - - "qualimap/$id" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--deseq2_output" - info: null - default: - - "deseq2_qc" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--multiqc_report" - info: null - default: - - "multiqc/multiqc_report.html" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--multiqc_data" - info: null - default: - - "multiqc/multiqc_data" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--multiqc_plots" - info: null - default: - - "multiqc/multiqc_plots" - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--multiqc_versions" - info: null - must_exist: true - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" - - type: "file" - name: "--versions" - info: null - must_exist: false - create_parent: true - required: false - direction: "output" - multiple: false - multiple_sep: ";" -resources: -- type: "nextflow_script" - path: "main.nf" - is_executable: true - entrypoint: "run_wf" -description: "A viash workflow for the nf-core/rnaseq pipeline.\n" -info: null -status: "enabled" -requirements: - commands: - - "ps" -dependencies: -- name: "workflows/prepare_genome" - repository: - type: "local" -- name: "cat_fastq" - repository: - type: "local" -- name: "workflows/pre_processing" - repository: - type: "local" -- name: "workflows/genome_alignment_and_quant" - repository: - type: "local" -- name: "workflows/pseudo_alignment_and_quant" - repository: - type: "local" -- name: "workflows/post_processing" - repository: - type: "local" -- name: "workflows/quality_control" - repository: - type: "local" -repositories: -- type: "vsh" - name: "biobox" - repo: "vsh/biobox" - tag: "v0.2.0" -- type: "vsh" - name: "craftbox" - repo: "craftbox" - tag: "v0.1.0" -runners: -- type: "executable" - id: "executable" - docker_setup_strategy: "ifneedbepullelsecachedbuild" -- type: "nextflow" - id: "nextflow" - directives: - tag: "$id" - auto: - simplifyInput: true - simplifyOutput: false - transcript: false - publish: false - config: - labels: - mem1gb: "memory = 1000000000.B" - mem2gb: "memory = 2000000000.B" - mem5gb: "memory = 5000000000.B" - mem10gb: "memory = 10000000000.B" - mem20gb: "memory = 20000000000.B" - mem50gb: "memory = 50000000000.B" - mem100gb: "memory = 100000000000.B" - mem200gb: "memory = 200000000000.B" - mem500gb: "memory = 500000000000.B" - mem1tb: "memory = 1000000000000.B" - mem2tb: "memory = 2000000000000.B" - mem5tb: "memory = 5000000000000.B" - mem10tb: "memory = 10000000000000.B" - mem20tb: "memory = 20000000000000.B" - mem50tb: "memory = 50000000000000.B" - mem100tb: "memory = 100000000000000.B" - mem200tb: "memory = 200000000000000.B" - mem500tb: "memory = 500000000000000.B" - mem1gib: "memory = 1073741824.B" - mem2gib: "memory = 2147483648.B" - mem4gib: "memory = 4294967296.B" - mem8gib: "memory = 8589934592.B" - mem16gib: "memory = 17179869184.B" - mem32gib: "memory = 34359738368.B" - mem64gib: "memory = 68719476736.B" - mem128gib: "memory = 137438953472.B" - mem256gib: "memory = 274877906944.B" - mem512gib: "memory = 549755813888.B" - mem1tib: "memory = 1099511627776.B" - mem2tib: "memory = 2199023255552.B" - mem4tib: "memory = 4398046511104.B" - mem8tib: "memory = 8796093022208.B" - mem16tib: "memory = 17592186044416.B" - mem32tib: "memory = 35184372088832.B" - mem64tib: "memory = 70368744177664.B" - mem128tib: "memory = 140737488355328.B" - mem256tib: "memory = 281474976710656.B" - mem512tib: "memory = 562949953421312.B" - cpu1: "cpus = 1" - cpu2: "cpus = 2" - cpu5: "cpus = 5" - cpu10: "cpus = 10" - cpu20: "cpus = 20" - cpu50: "cpus = 50" - cpu100: "cpus = 100" - cpu200: "cpus = 200" - cpu500: "cpus = 500" - cpu1000: "cpus = 1000" - debug: false - container: "docker" -engines: -- type: "native" - id: "native" -build_info: - config: "src/workflows/rnaseq/config.vsh.yaml" - runner: "nextflow" - engine: "native" - output: "target/nextflow/workflows/rnaseq" - executable: "target/nextflow/workflows/rnaseq/main.nf" - viash_version: "0.9.0" - git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" - git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" - dependencies: - - "target/nextflow/workflows/prepare_genome" - - "target/nextflow/cat_fastq" - - "target/nextflow/workflows/pre_processing" - - "target/nextflow/workflows/genome_alignment_and_quant" - - "target/nextflow/workflows/pseudo_alignment_and_quant" - - "target/nextflow/workflows/post_processing" - - "target/nextflow/workflows/quality_control" -package_config: - version: "multiple_fixes" - info: - test_resources: - - path: "gs://viash-hub-test-data/rnaseq/v1" - dest: "testData" - repositories: - - type: "vsh" - name: "biobox" - repo: "vsh/biobox" - tag: "v0.2.0" - - type: "vsh" - name: "craftbox" - repo: "craftbox" - tag: "v0.1.0" - viash_version: "0.9.0" - source: "src" - target: "target" - config_mods: - - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\ - \ := '$id'\n" - - ".engines += { type: \"native\" }" - - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'multiple_fixes'" - organization: "vsh" diff --git a/target/nextflow/workflows/rnaseq/main.nf b/target/nextflow/workflows/rnaseq/main.nf deleted file mode 100644 index 2349a37..0000000 --- a/target/nextflow/workflows/rnaseq/main.nf +++ /dev/null @@ -1,5907 +0,0 @@ -// rnaseq multiple_fixes -// -// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative -// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data -// Intuitive. -// -// The component may contain files which fall under a different license. The -// authors of this component should specify the license in the header of such -// files, or include a separate license file detailing the licenses of all included -// files. - -//////////////////////////// -// VDSL3 helper functions // -//////////////////////////// - -// helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_checkArgumentType.nf' -class UnexpectedArgumentTypeException extends Exception { - String errorIdentifier - String stage - String plainName - String expectedClass - String foundClass - - // ${key ? " in module '$key'" : ""}${id ? " id '$id'" : ""} - UnexpectedArgumentTypeException(String errorIdentifier, String stage, String plainName, String expectedClass, String foundClass) { - super("Error${errorIdentifier ? " $errorIdentifier" : ""}:${stage ? " $stage" : "" } argument '${plainName}' has the wrong type. " + - "Expected type: ${expectedClass}. Found type: ${foundClass}") - this.errorIdentifier = errorIdentifier - this.stage = stage - this.plainName = plainName - this.expectedClass = expectedClass - this.foundClass = foundClass - } -} - -/** - * Checks if the given value is of the expected type. If not, an exception is thrown. - * - * @param stage The stage of the argument (input or output) - * @param par The parameter definition - * @param value The value to check - * @param errorIdentifier The identifier to use in the error message - * @return The value, if it is of the expected type - * @throws UnexpectedArgumentTypeException If the value is not of the expected type -*/ -def _checkArgumentType(String stage, Map par, Object value, String errorIdentifier) { - // expectedClass will only be != null if value is not of the expected type - def expectedClass = null - def foundClass = null - - // todo: split if need be - - if (!par.required && value == null) { - expectedClass = null - } else if (par.multiple) { - if (value !instanceof Collection) { - value = [value] - } - - // split strings - value = value.collectMany{ val -> - if (val instanceof String) { - // collect() to ensure that the result is a List and not simply an array - val.split(par.multiple_sep).collect() - } else { - [val] - } - } - - // process globs - if (par.type == "file" && par.direction == "input") { - value = value.collect{ it instanceof String ? file(it, hidden: true) : it }.flatten() - } - - // check types of elements in list - try { - value = value.collect { listVal -> - _checkArgumentType(stage, par + [multiple: false], listVal, errorIdentifier) - } - } catch (UnexpectedArgumentTypeException e) { - expectedClass = "List[${e.expectedClass}]" - foundClass = "List[${e.foundClass}]" - } - } else if (par.type == "string") { - // cast to string if need be - if (value instanceof GString) { - value = value.toString() - } - expectedClass = value instanceof String ? null : "String" - } else if (par.type == "integer") { - // cast to integer if need be - if (value instanceof String) { - try { - value = value.toInteger() - } catch (NumberFormatException e) { - // do nothing - } - } - if (value instanceof java.math.BigInteger) { - value = value.intValue() - } - expectedClass = value instanceof Integer ? null : "Integer" - } else if (par.type == "long") { - // cast to long if need be - if (value instanceof String) { - try { - value = value.toLong() - } catch (NumberFormatException e) { - // do nothing - } - } - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" - } else if (par.type == "double") { - // cast to double if need be - if (value instanceof String) { - try { - value = value.toDouble() - } catch (NumberFormatException e) { - // do nothing - } - } - if (value instanceof java.math.BigDecimal) { - value = value.doubleValue() - } - if (value instanceof Float) { - value = value.toDouble() - } - expectedClass = value instanceof Double ? null : "Double" - } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { - // cast to boolean if need be - if (value instanceof String) { - def valueLower = value.toLowerCase() - if (valueLower == "true") { - value = true - } else if (valueLower == "false") { - value = false - } - } - expectedClass = value instanceof Boolean ? null : "Boolean" - } else if (par.type == "file" && (par.direction == "input" || stage == "output")) { - // cast to path if need be - if (value instanceof String) { - value = file(value, hidden: true) - } - if (value instanceof File) { - value = value.toPath() - } - expectedClass = value instanceof Path ? null : "Path" - } else if (par.type == "file" && stage == "input" && par.direction == "output") { - // cast to string if need be - if (value instanceof GString) { - value = value.toString() - } - expectedClass = value instanceof String ? null : "String" - } else { - // didn't find a match for par.type - expectedClass = par.type - } - - if (expectedClass != null) { - if (foundClass == null) { - foundClass = value.getClass().getName() - } - throw new UnexpectedArgumentTypeException(errorIdentifier, stage, par.plainName, expectedClass, foundClass) - } - - return value -} -// helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processInputValues.nf' -Map _processInputValues(Map inputs, Map config, String id, String key) { - if (!workflow.stubRun) { - config.allArguments.each { arg -> - if (arg.required) { - assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : - "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing" - } - } - - inputs = inputs.collectEntries { name, value -> - def par = config.allArguments.find { it.plainName == name && (it.direction == "input" || it.type == "file") } - assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid input argument" - - value = _checkArgumentType("input", par, value, "in module '$key' id '$id'") - - [ name, value ] - } - } - return inputs -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/arguments/_processOutputValues.nf' -Map _processOutputValues(Map outputs, Map config, String id, String key) { - if (!workflow.stubRun) { - config.allArguments.each { arg -> - if (arg.direction == "output" && arg.required) { - assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : - "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing" - } - } - - outputs = outputs.collectEntries { name, value -> - def par = config.allArguments.find { it.plainName == name && it.direction == "output" } - assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument" - - value = _checkArgumentType("output", par, value, "in module '$key' id '$id'") - - [ name, value ] - } - } - return outputs -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/IDChecker.nf' -class IDChecker { - final def items = [] as Set - - @groovy.transform.WithWriteLock - boolean observe(String item) { - if (items.contains(item)) { - return false - } else { - items << item - return true - } - } - - @groovy.transform.WithReadLock - boolean contains(String item) { - return items.contains(item) - } - - @groovy.transform.WithReadLock - Set getItems() { - return items.clone() - } -} -// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/_checkUniqueIds.nf' - -/** - * Check if the ids are unique across parameter sets - * - * @param parameterSets a list of parameter sets. - */ -private void _checkUniqueIds(List>> parameterSets) { - def ppIds = parameterSets.collect{it[0]} - assert ppIds.size() == ppIds.unique().size() : "All argument sets should have unique ids. Detected ids: $ppIds" -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/_getChild.nf' - -// helper functions for reading params from file // -def _getChild(parent, child) { - if (child.contains("://") || java.nio.file.Paths.get(child).isAbsolute()) { - child - } else { - def parentAbsolute = java.nio.file.Paths.get(parent).toAbsolutePath().toString() - parentAbsolute.replaceAll('/[^/]*$', "/") + child - } -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/_parseParamList.nf' -/** - * Figure out the param list format based on the file extension - * - * @param param_list A String containing the path to the parameter list file. - * - * @return A String containing the format of the parameter list file. - */ -def _paramListGuessFormat(param_list) { - if (param_list !instanceof String) { - "asis" - } else if (param_list.endsWith(".csv")) { - "csv" - } else if (param_list.endsWith(".json") || param_list.endsWith(".jsn")) { - "json" - } else if (param_list.endsWith(".yaml") || param_list.endsWith(".yml")) { - "yaml" - } else { - "yaml_blob" - } -} - - -/** - * Read the param list - * - * @param param_list One of the following: - * - A String containing the path to the parameter list file (csv, json or yaml), - * - A yaml blob of a list of maps (yaml_blob), - * - Or a groovy list of maps (asis). - * @param config A Map of the Viash configuration. - * - * @return A List of Maps containing the parameters. - */ -def _parseParamList(param_list, Map config) { - // first determine format by extension - def paramListFormat = _paramListGuessFormat(param_list) - - def paramListPath = (paramListFormat != "asis" && paramListFormat != "yaml_blob") ? - file(param_list, hidden: true) : - null - - // get the correct parser function for the detected params_list format - def paramSets = [] - if (paramListFormat == "asis") { - paramSets = param_list - } else if (paramListFormat == "yaml_blob") { - paramSets = readYamlBlob(param_list) - } else if (paramListFormat == "yaml") { - paramSets = readYaml(paramListPath) - } else if (paramListFormat == "json") { - paramSets = readJson(paramListPath) - } else if (paramListFormat == "csv") { - paramSets = readCsv(paramListPath) - } else { - error "Format of provided --param_list not recognised.\n" + - "Found: '$paramListFormat'.\n" + - "Expected: a csv file, a json file, a yaml file,\n" + - "a yaml blob or a groovy list of maps." - } - - // data checks - assert paramSets instanceof List: "--param_list should contain a list of maps" - for (value in paramSets) { - assert value instanceof Map: "--param_list should contain a list of maps" - } - - // id is argument - def idIsArgument = config.allArguments.any{it.plainName == "id"} - - // Reformat from List to List> by adding the ID as first element of a Tuple2 - paramSets = paramSets.collect({ data -> - def id = data.id - if (!idIsArgument) { - data = data.findAll{k, v -> k != "id"} - } - [id, data] - }) - - // Split parameters with 'multiple: true' - paramSets = paramSets.collect({ id, data -> - data = _splitParams(data, config) - [id, data] - }) - - // The paths of input files inside a param_list file may have been specified relatively to the - // location of the param_list file. These paths must be made absolute. - if (paramListPath) { - paramSets = paramSets.collect({ id, data -> - def new_data = data.collectEntries{ parName, parValue -> - def par = config.allArguments.find{it.plainName == parName} - if (par && par.type == "file" && par.direction == "input") { - if (parValue instanceof Collection) { - parValue = parValue.collectMany{path -> - def x = _resolveSiblingIfNotAbsolute(path, paramListPath) - x instanceof Collection ? x : [x] - } - } else { - parValue = _resolveSiblingIfNotAbsolute(parValue, paramListPath) - } - } - [parName, parValue] - } - [id, new_data] - }) - } - - return paramSets -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/_splitParams.nf' -/** - * Split parameters for arguments that accept multiple values using their separator - * - * @param paramList A Map containing parameters to split. - * @param config A Map of the Viash configuration. This Map can be generated from the config file - * using the readConfig() function. - * - * @return A Map of parameters where the parameter values have been split into a list using - * their seperator. - */ -Map _splitParams(Map parValues, Map config){ - def parsedParamValues = parValues.collectEntries { parName, parValue -> - def parameterSettings = config.allArguments.find({it.plainName == parName}) - - if (!parameterSettings) { - // if argument is not found, do not alter - return [parName, parValue] - } - if (parameterSettings.multiple) { // Check if parameter can accept multiple values - if (parValue instanceof Collection) { - parValue = parValue.collect{it instanceof String ? it.split(parameterSettings.multiple_sep) : it } - } else if (parValue instanceof String) { - parValue = parValue.split(parameterSettings.multiple_sep) - } else if (parValue == null) { - parValue = [] - } else { - parValue = [ parValue ] - } - parValue = parValue.flatten() - } - // For all parameters check if multiple values are only passed for - // arguments that allow it. Quietly simplify lists of length 1. - if (!parameterSettings.multiple && parValue instanceof Collection) { - assert parValue.size() == 1 : - "Error: argument ${parName} has too many values.\n" + - " Expected amount: 1. Found: ${parValue.size()}" - parValue = parValue[0] - } - [parName, parValue] - } - return parsedParamValues -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/channelFromParams.nf' -/** - * Parse nextflow parameters based on settings defined in a viash config. - * Return a list of parameter sets, each parameter set corresponding to - * an event in a nextflow channel. The output from this function can be used - * with Channel.fromList to create a nextflow channel with Vdsl3 formatted - * events. - * - * This function performs: - * - A filtering of the params which can be found in the config file. - * - Process the params_list argument which allows a user to to initialise - * a Vsdl3 channel with multiple parameter sets. Possible formats are - * csv, json, yaml, or simply a yaml_blob. A csv should have column names - * which correspond to the different arguments of this pipeline. A json or a yaml - * file should be a list of maps, each of which has keys corresponding to the - * arguments of the pipeline. A yaml blob can also be passed directly as a parameter. - * When passing a csv, json or yaml, relative path names are relativized to the - * location of the parameter file. - * - Combine the parameter sets into a vdsl3 Channel. - * - * @param params Input parameters. Can optionaly contain a 'param_list' key that - * provides a list of arguments that can be split up into multiple events - * in the output channel possible formats of param_lists are: a csv file, - * json file, a yaml file or a yaml blob. Each parameters set (event) must - * have a unique ID. - * @param config A Map of the Viash configuration. This Map can be generated from the config file - * using the readConfig() function. - * - * @return A list of parameters with the first element of the event being - * the event ID and the second element containing a map of the parsed parameters. - */ - -private List>> _paramsToParamSets(Map params, Map config){ - // todo: fetch key from run args - def key_ = config.name - - /* parse regular parameters (not in param_list) */ - /*************************************************/ - def globalParams = config.allArguments - .findAll { params.containsKey(it.plainName) } - .collectEntries { [ it.plainName, params[it.plainName] ] } - def globalID = params.get("id", null) - - /* process params_list arguments */ - /*********************************/ - def paramList = params.containsKey("param_list") && params.param_list != null ? - params.param_list : [] - // if (paramList instanceof String) { - // paramList = [paramList] - // } - // def paramSets = paramList.collectMany{ _parseParamList(it, config) } - // TODO: be able to process param_list when it is a list of strings - def paramSets = _parseParamList(paramList, config) - if (paramSets.isEmpty()) { - paramSets = [[null, [:]]] - } - - /* combine arguments into channel */ - /**********************************/ - def processedParams = paramSets.indexed().collect{ index, tup -> - // Process ID - def id = tup[0] ?: globalID - - if (workflow.stubRun && !id) { - // if stub run, explicitly add an id if missing - id = "stub${index}" - } - assert id != null: "Each parameter set should have at least an 'id'" - - // Process params - def parValues = globalParams + tup[1] - // // Remove parameters which are null, if the default is also null - // parValues = parValues.collectEntries{paramName, paramValue -> - // parameterSettings = config.functionality.allArguments.find({it.plainName == paramName}) - // if ( paramValue != null || parameterSettings.get("default", null) != null ) { - // [paramName, paramValue] - // } - // } - parValues = parValues.collectEntries { name, value -> - def par = config.allArguments.find { it.plainName == name && (it.direction == "input" || it.type == "file") } - assert par != null : "Error in module '${key_}' id '${id}': '${name}' is not a valid input argument" - - if (par == null) { - return [:] - } - value = _checkArgumentType("input", par, value, "in module '$key_' id '$id'") - - [ name, value ] - } - - [id, parValues] - } - - // Check if ids (first element of each list) is unique - _checkUniqueIds(processedParams) - return processedParams -} - -/** - * Parse nextflow parameters based on settings defined in a viash config - * and return a nextflow channel. - * - * @param params Input parameters. Can optionaly contain a 'param_list' key that - * provides a list of arguments that can be split up into multiple events - * in the output channel possible formats of param_lists are: a csv file, - * json file, a yaml file or a yaml blob. Each parameters set (event) must - * have a unique ID. - * @param config A Map of the Viash configuration. This Map can be generated from the config file - * using the readConfig() function. - * - * @return A nextflow Channel with events. Events are formatted as a tuple that contains - * first contains the ID of the event and as second element holds a parameter map. - * - * - */ -def channelFromParams(Map params, Map config) { - def processedParams = _paramsToParamSets(params, config) - return Channel.fromList(processedParams) -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/checkUniqueIds.nf' -def checkUniqueIds(Map args) { - def stopOnError = args.stopOnError == null ? args.stopOnError : true - - def idChecker = new IDChecker() - - return filter { tup -> - if (!idChecker.observe(tup[0])) { - if (stopOnError) { - error "Duplicate id: ${tup[0]}" - } else { - log.warn "Duplicate id: ${tup[0]}, removing duplicate entry" - return false - } - } - return true - } -} -// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/preprocessInputs.nf' -// This helper file will be deprecated soon -preprocessInputsDeprecationWarningPrinted = false - -def preprocessInputsDeprecationWarning() { - if (!preprocessInputsDeprecationWarningPrinted) { - preprocessInputsDeprecationWarningPrinted = true - System.err.println("Warning: preprocessInputs() is deprecated and will be removed in Viash 0.9.0.") - } -} - -/** - * Generate a nextflow Workflow that allows processing a channel of - * Vdsl3 formatted events and apply a Viash config to them: - * - Gather default parameters from the Viash config and make - * sure that they are correctly formatted (see applyConfig method). - * - Format the input parameters (also using the applyConfig method). - * - Apply the default parameter to the input parameters. - * - Do some assertions: - * ~ Check if the event IDs in the channel are unique. - * - * The events in the channel are formatted as tuples, with the - * first element of the tuples being a unique id of the parameter set, - * and the second element containg the the parameters themselves. - * Optional extra elements of the tuples will be passed to the output as is. - * - * @param args A map that must contain a 'config' key that points - * to a parsed config (see readConfig()). Optionally, a - * 'key' key can be provided which can be used to create a unique - * name for the workflow process. - * - * @return A workflow that allows processing a channel of Vdsl3 formatted events - * and apply a Viash config to them. - */ -def preprocessInputs(Map args) { - preprocessInputsDeprecationWarning() - - def config = args.config - assert config instanceof Map : - "Error in preprocessInputs: config must be a map. " + - "Expected class: Map. Found: config.getClass() is ${config.getClass()}" - def key_ = args.key ?: config.name - - // Get different parameter types (used throughout this function) - def defaultArgs = config.allArguments - .findAll { it.containsKey("default") } - .collectEntries { [ it.plainName, it.default ] } - - map { tup -> - def id = tup[0] - def data = tup[1] - def passthrough = tup.drop(2) - - def new_data = (defaultArgs + data).collectEntries { name, value -> - def par = config.allArguments.find { it.plainName == name && (it.direction == "input" || it.type == "file") } - - if (par != null) { - value = _checkArgumentType("input", par, value, "in module '$key_' id '$id'") - } - - [ name, value ] - } - - [ id, new_data ] + passthrough - } -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/runComponents.nf' -/** - * Run a list of components on a stream of data. - * - * @param components: list of Viash VDSL3 modules to run - * @param fromState: a closure, a map or a list of keys to extract from the input data. - * If a closure, it will be called with the id, the data and the component config. - * @param toState: a closure, a map or a list of keys to extract from the output data - * If a closure, it will be called with the id, the output data, the old state and the component config. - * @param filter: filter function to apply to the input. - * It will be called with the id, the data and the component config. - * @param id: id to use for the output data - * If a closure, it will be called with the id, the data and the component config. - * @param auto: auto options to pass to the components - * - * @return: a workflow that runs the components - **/ -def runComponents(Map args) { - log.warn("runComponents is deprecated, use runEach instead") - assert args.components: "runComponents should be passed a list of components to run" - - def components_ = args.components - if (components_ !instanceof List) { - components_ = [ components_ ] - } - assert components_.size() > 0: "pass at least one component to runComponents" - - def fromState_ = args.fromState - def toState_ = args.toState - def filter_ = args.filter - def id_ = args.id - - workflow runComponentsWf { - take: input_ch - main: - - // generate one channel per method - out_chs = components_.collect{ comp_ -> - def comp_config = comp_.config - - def filter_ch = filter_ - ? input_ch | filter{tup -> - filter_(tup[0], tup[1], comp_config) - } - : input_ch - def id_ch = id_ - ? filter_ch | map{tup -> - // def new_id = id_(tup[0], tup[1], comp_config) - def new_id = tup[0] - if (id_ instanceof String) { - new_id = id_ - } else if (id_ instanceof Closure) { - new_id = id_(new_id, tup[1], comp_config) - } - [new_id] + tup.drop(1) - } - : filter_ch - def data_ch = id_ch | map{tup -> - def new_data = tup[1] - if (fromState_ instanceof Map) { - new_data = fromState_.collectEntries{ key0, key1 -> - [key0, new_data[key1]] - } - } else if (fromState_ instanceof List) { - new_data = fromState_.collectEntries{ key -> - [key, new_data[key]] - } - } else if (fromState_ instanceof Closure) { - new_data = fromState_(tup[0], new_data, comp_config) - } - tup.take(1) + [new_data] + tup.drop(1) - } - def out_ch = data_ch - | comp_.run( - auto: (args.auto ?: [:]) + [simplifyInput: false, simplifyOutput: false] - ) - def post_ch = toState_ - ? out_ch | map{tup -> - def output = tup[1] - def old_state = tup[2] - def new_state = null - if (toState_ instanceof Map) { - new_state = old_state + toState_.collectEntries{ key0, key1 -> - [key0, output[key1]] - } - } else if (toState_ instanceof List) { - new_state = old_state + toState_.collectEntries{ key -> - [key, output[key]] - } - } else if (toState_ instanceof Closure) { - new_state = toState_(tup[0], output, old_state, comp_config) - } - [tup[0], new_state] + tup.drop(3) - } - : out_ch - - post_ch - } - - // mix all results - output_ch = - (out_chs.size == 1) - ? out_chs[0] - : out_chs[0].mix(*out_chs.drop(1)) - - emit: output_ch - } - - return runComponentsWf -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/runEach.nf' -/** - * Run a list of components on a stream of data. - * - * @param components: list of Viash VDSL3 modules to run - * @param fromState: a closure, a map or a list of keys to extract from the input data. - * If a closure, it will be called with the id, the data and the component itself. - * @param toState: a closure, a map or a list of keys to extract from the output data - * If a closure, it will be called with the id, the output data, the old state and the component itself. - * @param filter: filter function to apply to the input. - * It will be called with the id, the data and the component itself. - * @param id: id to use for the output data - * If a closure, it will be called with the id, the data and the component itself. - * @param auto: auto options to pass to the components - * - * @return: a workflow that runs the components - **/ -def runEach(Map args) { - assert args.components: "runEach should be passed a list of components to run" - - def components_ = args.components - if (components_ !instanceof List) { - components_ = [ components_ ] - } - assert components_.size() > 0: "pass at least one component to runEach" - - def fromState_ = args.fromState - def toState_ = args.toState - def filter_ = args.filter - def runIf_ = args.runIf - def id_ = args.id - - assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf." - - workflow runEachWf { - take: input_ch - main: - - // generate one channel per method - out_chs = components_.collect{ comp_ -> - def filter_ch = filter_ - ? input_ch | filter{tup -> - filter_(tup[0], tup[1], comp_) - } - : input_ch - def id_ch = id_ - ? filter_ch | map{tup -> - def new_id = id_ - if (new_id instanceof Closure) { - new_id = new_id(tup[0], tup[1], comp_) - } - assert new_id instanceof String : "Error in runEach: id should be a String or a Closure that returns a String. Expected: id instanceof String. Found: ${new_id.getClass()}" - [new_id] + tup.drop(1) - } - : filter_ch - def chPassthrough = null - def chRun = null - if (runIf_) { - def idRunIfBranch = id_ch.branch{ tup -> - run: runIf_(tup[0], tup[1], comp_) - passthrough: true - } - chPassthrough = idRunIfBranch.passthrough - chRun = idRunIfBranch.run - } else { - chRun = id_ch - chPassthrough = Channel.empty() - } - def data_ch = chRun | map{tup -> - def new_data = tup[1] - if (fromState_ instanceof Map) { - new_data = fromState_.collectEntries{ key0, key1 -> - [key0, new_data[key1]] - } - } else if (fromState_ instanceof List) { - new_data = fromState_.collectEntries{ key -> - [key, new_data[key]] - } - } else if (fromState_ instanceof Closure) { - new_data = fromState_(tup[0], new_data, comp_) - } - tup.take(1) + [new_data] + tup.drop(1) - } - def out_ch = data_ch - | comp_.run( - auto: (args.auto ?: [:]) + [simplifyInput: false, simplifyOutput: false] - ) - def post_ch = toState_ - ? out_ch | map{tup -> - def output = tup[1] - def old_state = tup[2] - def new_state = null - if (toState_ instanceof Map) { - new_state = old_state + toState_.collectEntries{ key0, key1 -> - [key0, output[key1]] - } - } else if (toState_ instanceof List) { - new_state = old_state + toState_.collectEntries{ key -> - [key, output[key]] - } - } else if (toState_ instanceof Closure) { - new_state = toState_(tup[0], output, old_state, comp_) - } - [tup[0], new_state] + tup.drop(3) - } - : out_ch - - def return_ch = post_ch - | concat(chPassthrough) - - return_ch - } - - // mix all results - output_ch = - (out_chs.size == 1) - ? out_chs[0] - : out_chs[0].mix(*out_chs.drop(1)) - - emit: output_ch - } - - return runEachWf -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/channel/safeJoin.nf' -/** - * Join sourceChannel to targetChannel - * - * This function joins the sourceChannel to the targetChannel. - * However, each id in the targetChannel must be present in the - * sourceChannel. If _meta.join_id exists in the targetChannel, that is - * used as an id instead. If the id doesn't match any id in the sourceChannel, - * an error is thrown. - */ - -def safeJoin(targetChannel, sourceChannel, key) { - def sourceIDs = new IDChecker() - - def sourceCheck = sourceChannel - | map { tup -> - sourceIDs.observe(tup[0]) - tup - } - def targetCheck = targetChannel - | map { tup -> - def id = tup[0] - - if (!sourceIDs.contains(id)) { - error ( - "Error in module '${key}' when merging output with original state.\n" + - " Reason: output with id '${id}' could not be joined with source channel.\n" + - " If the IDs in the output channel differ from the input channel,\n" + - " please set `tup[1]._meta.join_id to the original ID.\n" + - " Original IDs in input channel: ['${sourceIDs.getItems().join("', '")}'].\n" + - " Unexpected ID in the output channel: '${id}'.\n" + - " Example input event: [\"id\", [input: file(...)]],\n" + - " Example output event: [\"newid\", [output: file(...), _meta: [join_id: \"id\"]]]" - ) - } - // TODO: add link to our documentation on how to fix this - - tup - } - - sourceCheck.cross(targetChannel) - | map{ left, right -> - right + left.drop(1) - } -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/config/_processArgument.nf' -def _processArgument(arg) { - arg.multiple = arg.multiple != null ? arg.multiple : false - arg.required = arg.required != null ? arg.required : false - arg.direction = arg.direction != null ? arg.direction : "input" - arg.multiple_sep = arg.multiple_sep != null ? arg.multiple_sep : ";" - arg.plainName = arg.name.replaceAll("^-*", "") - - if (arg.type == "file") { - arg.must_exist = arg.must_exist != null ? arg.must_exist : true - arg.create_parent = arg.create_parent != null ? arg.create_parent : true - } - - // add default values to output files which haven't already got a default - if (arg.type == "file" && arg.direction == "output" && arg.default == null) { - def mult = arg.multiple ? "_*" : "" - def extSearch = "" - if (arg.default != null) { - extSearch = arg.default - } else if (arg.example != null) { - extSearch = arg.example - } - if (extSearch instanceof List) { - extSearch = extSearch[0] - } - def extSearchResult = extSearch.find("\\.[^\\.]+\$") - def ext = extSearchResult != null ? extSearchResult : "" - arg.default = "\$id.\$key.${arg.plainName}${mult}${ext}" - if (arg.multiple) { - arg.default = [arg.default] - } - } - - if (!arg.multiple) { - if (arg.default != null && arg.default instanceof List) { - arg.default = arg.default[0] - } - if (arg.example != null && arg.example instanceof List) { - arg.example = arg.example[0] - } - } - - if (arg.type == "boolean_true") { - arg.default = false - } - if (arg.type == "boolean_false") { - arg.default = true - } - - arg -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/config/addGlobalParams.nf' -def addGlobalArguments(config) { - def localConfig = [ - "argument_groups": [ - [ - "name": "Nextflow input-output arguments", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "arguments" : [ - [ - 'name': '--publish_dir', - 'required': true, - 'type': 'string', - 'description': 'Path to an output directory.', - 'example': 'output/', - 'multiple': false - ], - [ - 'name': '--param_list', - 'required': false, - 'type': 'string', - 'description': '''Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob. - | - |* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ ['id': 'foo', 'input': 'foo.txt'], ['id': 'bar', 'input': 'bar.txt'] ]`. - |* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`. - |* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {'id': 'foo', 'input': 'foo.txt'}, {'id': 'bar', 'input': 'bar.txt'} ]`. - |* A yaml blob can also be passed directly as a string. Example: `--param_list "[ {'id': 'foo', 'input': 'foo.txt'}, {'id': 'bar', 'input': 'bar.txt'} ]"`. - | - |When passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.'''.stripMargin(), - 'example': 'my_params.yaml', - 'multiple': false, - 'hidden': true - ] - // TODO: allow multiple: true in param_list? - // TODO: allow to specify a --param_list_regex to filter the param_list? - // TODO: allow to specify a --param_list_from_state to remap entries in the param_list? - ] - ] - ] - ] - - return processConfig(_mergeMap(config, localConfig)) -} - -def _mergeMap(Map lhs, Map rhs) { - return rhs.inject(lhs.clone()) { map, entry -> - if (map[entry.key] instanceof Map && entry.value instanceof Map) { - map[entry.key] = _mergeMap(map[entry.key], entry.value) - } else if (map[entry.key] instanceof Collection && entry.value instanceof Collection) { - map[entry.key] += entry.value - } else { - map[entry.key] = entry.value - } - return map - } -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/config/generateHelp.nf' -def _generateArgumentHelp(param) { - // alternatives are not supported - // def names = param.alternatives ::: List(param.name) - - def unnamedProps = [ - ["required parameter", param.required], - ["multiple values allowed", param.multiple], - ["output", param.direction.toLowerCase() == "output"], - ["file must exist", param.type == "file" && param.must_exist] - ].findAll{it[1]}.collect{it[0]} - - def dflt = null - if (param.default != null) { - if (param.default instanceof List) { - dflt = param.default.join(param.multiple_sep != null ? param.multiple_sep : ", ") - } else { - dflt = param.default.toString() - } - } - def example = null - if (param.example != null) { - if (param.example instanceof List) { - example = param.example.join(param.multiple_sep != null ? param.multiple_sep : ", ") - } else { - example = param.example.toString() - } - } - def min = param.min?.toString() - def max = param.max?.toString() - - def escapeChoice = { choice -> - def s1 = choice.replaceAll("\\n", "\\\\n") - def s2 = s1.replaceAll("\"", """\\\"""") - s2.contains(",") || s2 != choice ? "\"" + s2 + "\"" : s2 - } - def choices = param.choices == null ? - null : - "[ " + param.choices.collect{escapeChoice(it.toString())}.join(", ") + " ]" - - def namedPropsStr = [ - ["type", ([param.type] + unnamedProps).join(", ")], - ["default", dflt], - ["example", example], - ["choices", choices], - ["min", min], - ["max", max] - ] - .findAll{it[1]} - .collect{"\n " + it[0] + ": " + it[1].replaceAll("\n", "\\n")} - .join("") - - def descStr = param.description == null ? - "" : - _paragraphWrap("\n" + param.description.trim(), 80 - 8).join("\n ") - - "\n --" + param.plainName + - namedPropsStr + - descStr -} - -// Based on Helper.generateHelp() in Helper.scala -def _generateHelp(config) { - def fun = config - - // PART 1: NAME AND VERSION - def nameStr = fun.name + - (fun.version == null ? "" : " " + fun.version) - - // PART 2: DESCRIPTION - def descrStr = fun.description == null ? - "" : - "\n\n" + _paragraphWrap(fun.description.trim(), 80).join("\n") - - // PART 3: Usage - def usageStr = fun.usage == null ? - "" : - "\n\nUsage:\n" + fun.usage.trim() - - // PART 4: Options - def argGroupStrs = fun.allArgumentGroups.collect{argGroup -> - def name = argGroup.name - def descriptionStr = argGroup.description == null ? - "" : - "\n " + _paragraphWrap(argGroup.description.trim(), 80-4).join("\n ") + "\n" - def arguments = argGroup.arguments.collect{arg -> - arg instanceof String ? fun.allArguments.find{it.plainName == arg} : arg - }.findAll{it != null} - def argumentStrs = arguments.collect{param -> _generateArgumentHelp(param)} - - "\n\n$name:" + - descriptionStr + - argumentStrs.join("\n") - } - - // FINAL: combine - def out = nameStr + - descrStr + - usageStr + - argGroupStrs.join("") - - return out -} - -// based on Format._paragraphWrap -def _paragraphWrap(str, maxLength) { - def outLines = [] - str.split("\n").each{par -> - def words = par.split("\\s").toList() - - def word = null - def line = words.pop() - while(!words.isEmpty()) { - word = words.pop() - if (line.length() + word.length() + 1 <= maxLength) { - line = line + " " + word - } else { - outLines.add(line) - line = word - } - } - if (words.isEmpty()) { - outLines.add(line) - } - } - return outLines -} - -def helpMessage(config) { - if (params.containsKey("help") && params.help) { - def mergedConfig = addGlobalArguments(config) - def helpStr = _generateHelp(mergedConfig) - println(helpStr) - exit 0 - } -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/config/processConfig.nf' -def processConfig(config) { - // set defaults for arguments - config.arguments = - (config.arguments ?: []).collect{_processArgument(it)} - - // set defaults for argument_group arguments - config.argument_groups = - (config.argument_groups ?: []).collect{grp -> - grp.arguments = (grp.arguments ?: []).collect{_processArgument(it)} - grp - } - - // create combined arguments list - config.allArguments = - config.arguments + - config.argument_groups.collectMany{it.arguments} - - // add missing argument groups (based on Functionality::allArgumentGroups()) - def argGroups = config.argument_groups - if (argGroups.any{it.name.toLowerCase() == "arguments"}) { - argGroups = argGroups.collect{ grp -> - if (grp.name.toLowerCase() == "arguments") { - grp = grp + [ - arguments: grp.arguments + config.arguments - ] - } - grp - } - } else { - argGroups = argGroups + [ - name: "Arguments", - arguments: config.arguments - ] - } - config.allArgumentGroups = argGroups - - config -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/config/readConfig.nf' - -def readConfig(file) { - def config = readYaml(file ?: moduleDir.resolve("config.vsh.yaml")) - processConfig(config) -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/_resolveSiblingIfNotAbsolute.nf' -/** - * Resolve a path relative to the current file. - * - * @param str The path to resolve, as a String. - * @param parentPath The path to resolve relative to, as a Path. - * - * @return The path that may have been resovled, as a Path. - */ -def _resolveSiblingIfNotAbsolute(str, parentPath) { - if (str !instanceof String) { - return str - } - if (!_stringIsAbsolutePath(str)) { - return parentPath.resolveSibling(str) - } else { - return file(str, hidden: true) - } -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/_stringIsAbsolutePath.nf' -/** - * Check whether a path as a string is absolute. - * - * In the past, we tried using `file(., relative: true).isAbsolute()`, - * but the 'relative' option was added in 22.10.0. - * - * @param path The path to check, as a String. - * - * @return Whether the path is absolute, as a boolean. - */ -def _stringIsAbsolutePath(path) { - def _resolve_URL_PROTOCOL = ~/^([a-zA-Z][a-zA-Z0-9]*:)?\\/.+/ - - assert path instanceof String - return _resolve_URL_PROTOCOL.matcher(path).matches() -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/collectTraces.nf' -class CustomTraceObserver implements nextflow.trace.TraceObserver { - List traces - - CustomTraceObserver(List traces) { - this.traces = traces - } - - @Override - void onProcessComplete(nextflow.processor.TaskHandler handler, nextflow.trace.TraceRecord trace) { - def trace2 = trace.store.clone() - trace2.script = null - traces.add(trace2) - } - - @Override - void onProcessCached(nextflow.processor.TaskHandler handler, nextflow.trace.TraceRecord trace) { - def trace2 = trace.store.clone() - trace2.script = null - traces.add(trace2) - } -} - -def collectTraces() { - def traces = Collections.synchronizedList([]) - - // add custom trace observer which stores traces in the traces object - session.observers.add(new CustomTraceObserver(traces)) - - traces -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/deepClone.nf' -/** - * Performs a deep clone of the given object. - * @param x an object - */ -def deepClone(x) { - iterateMap(x, {it instanceof Cloneable ? it.clone() : it}) -} -// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/getPublishDir.nf' -def getPublishDir() { - return params.containsKey("publish_dir") ? params.publish_dir : - params.containsKey("publishDir") ? params.publishDir : - null -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/getRootDir.nf' - -// Recurse upwards until we find a '.build.yaml' file -def _findBuildYamlFile(pathPossiblySymlink) { - def path = pathPossiblySymlink.toRealPath() - def child = path.resolve(".build.yaml") - if (java.nio.file.Files.isDirectory(path) && java.nio.file.Files.exists(child)) { - return child - } else { - def parent = path.getParent() - if (parent == null) { - return null - } else { - return _findBuildYamlFile(parent) - } - } -} - -// get the root of the target folder -def getRootDir() { - def dir = _findBuildYamlFile(meta.resources_dir) - assert dir != null: "Could not find .build.yaml in the folder structure" - dir.getParent() -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/iterateMap.nf' -/** - * Recursively apply a function over the leaves of an object. - * @param obj The object to iterate over. - * @param fun The function to apply to each value. - * @return The object with the function applied to each value. - */ -def iterateMap(obj, fun) { - if (obj instanceof List && obj !instanceof String) { - return obj.collect{item -> - iterateMap(item, fun) - } - } else if (obj instanceof Map) { - return obj.collectEntries{key, item -> - [key.toString(), iterateMap(item, fun)] - } - } else { - return fun(obj) - } -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/functions/niceView.nf' -/** - * A view for printing the event of each channel as a YAML blob. - * This is useful for debugging. - */ -def niceView() { - workflow niceViewWf { - take: input - main: - output = input - | view{toYamlBlob(it)} - emit: output - } - return niceViewWf -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readCsv.nf' - -def readCsv(file_path) { - def output = [] - def inputFile = file_path !instanceof Path ? file(file_path, hidden: true) : file_path - - // todo: allow escaped quotes in string - // todo: allow single quotes? - def splitRegex = java.util.regex.Pattern.compile(''',(?=(?:[^"]*"[^"]*")*[^"]*$)''') - def removeQuote = java.util.regex.Pattern.compile('''"(.*)"''') - - def br = java.nio.file.Files.newBufferedReader(inputFile) - - def row = -1 - def header = null - while (br.ready() && header == null) { - def line = br.readLine() - row++ - if (!line.startsWith("#")) { - header = splitRegex.split(line, -1).collect{field -> - m = removeQuote.matcher(field) - m.find() ? m.replaceFirst('$1') : field - } - } - } - assert header != null: "CSV file should contain a header" - - while (br.ready()) { - def line = br.readLine() - row++ - if (line == null) { - br.close() - break - } - - if (!line.startsWith("#")) { - def predata = splitRegex.split(line, -1) - def data = predata.collect{field -> - if (field == "") { - return null - } - def m = removeQuote.matcher(field) - if (m.find()) { - return m.replaceFirst('$1') - } else { - return field - } - } - assert header.size() == data.size(): "Row $row should contain the same number as fields as the header" - - def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null} - output.add(dataMap) - } - } - - output -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readJson.nf' -def readJson(file_path) { - def inputFile = file_path !instanceof Path ? file(file_path, hidden: true) : file_path - def jsonSlurper = new groovy.json.JsonSlurper() - jsonSlurper.parse(inputFile) -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readJsonBlob.nf' -def readJsonBlob(str) { - def jsonSlurper = new groovy.json.JsonSlurper() - jsonSlurper.parseText(str) -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readTaggedYaml.nf' -// Custom constructor to modify how certain objects are parsed from YAML -class CustomConstructor extends org.yaml.snakeyaml.constructor.Constructor { - Path root - - class ConstructPath extends org.yaml.snakeyaml.constructor.AbstractConstruct { - public Object construct(org.yaml.snakeyaml.nodes.Node node) { - String filename = (String) constructScalar(node); - if (root != null) { - return root.resolve(filename); - } - return java.nio.file.Paths.get(filename); - } - } - - CustomConstructor(org.yaml.snakeyaml.LoaderOptions options, Path root) { - super(options) - this.root = root - // Handling !file tag and parse it back to a File type - this.yamlConstructors.put(new org.yaml.snakeyaml.nodes.Tag("!file"), new ConstructPath()) - } -} - -def readTaggedYaml(Path path) { - def options = new org.yaml.snakeyaml.LoaderOptions() - def constructor = new CustomConstructor(options, path.getParent()) - def yaml = new org.yaml.snakeyaml.Yaml(constructor) - return yaml.load(path.text) -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readYaml.nf' -def readYaml(file_path) { - def inputFile = file_path !instanceof Path ? file(file_path, hidden: true) : file_path - def yamlSlurper = new org.yaml.snakeyaml.Yaml() - yamlSlurper.load(inputFile) -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/readYamlBlob.nf' -def readYamlBlob(str) { - def yamlSlurper = new org.yaml.snakeyaml.Yaml() - yamlSlurper.load(str) -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/toJsonBlob.nf' -String toJsonBlob(data) { - return groovy.json.JsonOutput.toJson(data) -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/toTaggedYamlBlob.nf' -// Custom representer to modify how certain objects are represented in YAML -class CustomRepresenter extends org.yaml.snakeyaml.representer.Representer { - Path relativizer - - class RepresentPath implements org.yaml.snakeyaml.representer.Represent { - public String getFileName(Object obj) { - if (obj instanceof File) { - obj = ((File) obj).toPath(); - } - if (obj !instanceof Path) { - throw new IllegalArgumentException("Object: " + obj + " is not a Path or File"); - } - def path = (Path) obj; - - if (relativizer != null) { - return relativizer.relativize(path).toString() - } else { - return path.toString() - } - } - - public org.yaml.snakeyaml.nodes.Node representData(Object data) { - String filename = getFileName(data); - def tag = new org.yaml.snakeyaml.nodes.Tag("!file"); - return representScalar(tag, filename); - } - } - CustomRepresenter(org.yaml.snakeyaml.DumperOptions options, Path relativizer) { - super(options) - this.relativizer = relativizer - this.representers.put(sun.nio.fs.UnixPath, new RepresentPath()) - this.representers.put(Path, new RepresentPath()) - this.representers.put(File, new RepresentPath()) - } -} - -String toTaggedYamlBlob(data) { - return toRelativeTaggedYamlBlob(data, null) -} -String toRelativeTaggedYamlBlob(data, Path relativizer) { - def options = new org.yaml.snakeyaml.DumperOptions() - options.setDefaultFlowStyle(org.yaml.snakeyaml.DumperOptions.FlowStyle.BLOCK) - def representer = new CustomRepresenter(options, relativizer) - def yaml = new org.yaml.snakeyaml.Yaml(representer, options) - return yaml.dump(data) -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/toYamlBlob.nf' -String toYamlBlob(data) { - def options = new org.yaml.snakeyaml.DumperOptions() - options.setDefaultFlowStyle(org.yaml.snakeyaml.DumperOptions.FlowStyle.BLOCK) - options.setPrettyFlow(true) - def yaml = new org.yaml.snakeyaml.Yaml(options) - def cleanData = iterateMap(data, { it instanceof Path ? it.toString() : it }) - return yaml.dump(cleanData) -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/writeJson.nf' -void writeJson(data, file) { - assert data: "writeJson: data should not be null" - assert file: "writeJson: file should not be null" - file.write(toJsonBlob(data)) -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/readwrite/writeYaml.nf' -void writeYaml(data, file) { - assert data: "writeYaml: data should not be null" - assert file: "writeYaml: file should not be null" - file.write(toYamlBlob(data)) -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/states/findStates.nf' -def findStates(Map params, Map config) { - def auto_config = deepClone(config) - def auto_params = deepClone(params) - - auto_config = auto_config.clone() - // override arguments - auto_config.argument_groups = [] - auto_config.arguments = [ - [ - type: "string", - name: "--id", - description: "A dummy identifier", - required: false - ], - [ - type: "file", - name: "--input_states", - example: "/path/to/input/directory/**/state.yaml", - description: "Path to input directory containing the datasets to be integrated.", - required: true, - multiple: true, - multiple_sep: ";" - ], - [ - type: "string", - name: "--filter", - example: "foo/.*/state.yaml", - description: "Regex to filter state files by path.", - required: false - ], - // to do: make this a yaml blob? - [ - type: "string", - name: "--rename_keys", - example: ["newKey1:oldKey1", "newKey2:oldKey2"], - description: "Rename keys in the detected input files. This is useful if the input files do not match the set of input arguments of the workflow.", - required: false, - multiple: true, - multiple_sep: ";" - ], - [ - type: "string", - name: "--settings", - example: '{"output_dataset": "dataset.h5ad", "k": 10}', - description: "Global arguments as a JSON glob to be passed to all components.", - required: false - ] - ] - if (!(auto_params.containsKey("id"))) { - auto_params["id"] = "auto" - } - - // run auto config through processConfig once more - auto_config = processConfig(auto_config) - - workflow findStatesWf { - helpMessage(auto_config) - - output_ch = - channelFromParams(auto_params, auto_config) - | flatMap { autoId, args -> - - def globalSettings = args.settings ? readYamlBlob(args.settings) : [:] - - // look for state files in input dir - def stateFiles = args.input_states - - // filter state files by regex - if (args.filter) { - stateFiles = stateFiles.findAll{ stateFile -> - def stateFileStr = stateFile.toString() - def matcher = stateFileStr =~ args.filter - matcher.matches()} - } - - // read in states - def states = stateFiles.collect { stateFile -> - def state_ = readTaggedYaml(stateFile) - [state_.id, state_] - } - - // construct renameMap - if (args.rename_keys) { - def renameMap = args.rename_keys.collectEntries{renameString -> - def split = renameString.split(":") - assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values" - split - } - - // rename keys in state, only let states through which have all keys - // also add global settings - states = states.collectMany{id, state -> - def newState = [:] - - for (key in renameMap.keySet()) { - def origKey = renameMap[key] - if (!(state.containsKey(origKey))) { - return [] - } - newState[key] = state[origKey] - } - - [[id, globalSettings + newState]] - } - } - - states - } - emit: - output_ch - } - - return findStatesWf -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/states/joinStates.nf' -def joinStates(Closure apply_) { - workflow joinStatesWf { - take: input_ch - main: - output_ch = input_ch - | toSortedList - | filter{ it.size() > 0 } - | map{ tups -> - def ids = tups.collect{it[0]} - def states = tups.collect{it[1]} - apply_(ids, states) - } - - emit: output_ch - } - return joinStatesWf -} -// helper file: 'src/main/resources/io/viash/runners/nextflow/states/publishStates.nf' -def collectFiles(obj) { - if (obj instanceof java.io.File || obj instanceof Path) { - return [obj] - } else if (obj instanceof List && obj !instanceof String) { - return obj.collectMany{item -> - collectFiles(item) - } - } else if (obj instanceof Map) { - return obj.collectMany{key, item -> - collectFiles(item) - } - } else { - return [] - } -} - -/** - * Recurse through a state and collect all input files and their target output filenames. - * @param obj The state to recurse through. - * @param prefix The prefix to prepend to the output filenames. - */ -def collectInputOutputPaths(obj, prefix) { - if (obj instanceof File || obj instanceof Path) { - def path = obj instanceof Path ? obj : obj.toPath() - def ext = path.getFileName().toString().find("\\.[^\\.]+\$") ?: "" - def newFilename = prefix + ext - return [[obj, newFilename]] - } else if (obj instanceof List && obj !instanceof String) { - return obj.withIndex().collectMany{item, ix -> - collectInputOutputPaths(item, prefix + "_" + ix) - } - } else if (obj instanceof Map) { - return obj.collectMany{key, item -> - collectInputOutputPaths(item, prefix + "." + key) - } - } else { - return [] - } -} - -def publishStates(Map args) { - def key_ = args.get("key") - def yamlTemplate_ = args.get("output_state", args.get("outputState", '$id.$key.state.yaml')) - - assert key_ != null : "publishStates: key must be specified" - - workflow publishStatesWf { - take: input_ch - main: - input_ch - | map { tup -> - def id_ = tup[0] - def state_ = tup[1] - - // the input files and the target output filenames - def inputoutputFilenames_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose() - def inputFiles_ = inputoutputFilenames_[0] - def outputFilenames_ = inputoutputFilenames_[1] - - def yamlFilename = yamlTemplate_ - .replaceAll('\\$id', id_) - .replaceAll('\\$\\{id\\}', id_) - .replaceAll('\\$key', key_) - .replaceAll('\\$\\{key\\}', key_) - - // TODO: do the pathnames in state_ match up with the outputFilenames_? - - // convert state to yaml blob - def yamlBlob_ = toRelativeTaggedYamlBlob([id: id_] + state_, java.nio.file.Paths.get(yamlFilename)) - - [id_, yamlBlob_, yamlFilename, inputFiles_, outputFilenames_] - } - | publishStatesProc - emit: input_ch - } - return publishStatesWf -} -process publishStatesProc { - // todo: check publishpath? - publishDir path: "${getPublishDir()}/", mode: "copy" - tag "$id" - input: - tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles) - output: - tuple val(id), path{[yamlFile] + outputFiles} - script: - def copyCommands = [ - inputFiles instanceof List ? inputFiles : [inputFiles], - outputFiles instanceof List ? outputFiles : [outputFiles] - ] - .transpose() - .collectMany{infile, outfile -> - if (infile.toString() != outfile.toString()) { - [ - "[ -d \"\$(dirname '${outfile.toString()}')\" ] || mkdir -p \"\$(dirname '${outfile.toString()}')\"", - "cp -r '${infile.toString()}' '${outfile.toString()}'" - ] - } else { - // no need to copy if infile is the same as outfile - [] - } - } - """ -mkdir -p "\$(dirname '${yamlFile}')" -echo "Storing state as yaml" -echo '${yamlBlob}' > '${yamlFile}' -echo "Copying output files to destination folder" -${copyCommands.join("\n ")} -""" -} - - -// this assumes that the state contains no other values other than those specified in the config -def publishStatesByConfig(Map args) { - def config = args.get("config") - assert config != null : "publishStatesByConfig: config must be specified" - - def key_ = args.get("key", config.name) - assert key_ != null : "publishStatesByConfig: key must be specified" - - workflow publishStatesSimpleWf { - take: input_ch - main: - input_ch - | map { tup -> - def id_ = tup[0] - def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10] - def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad'] - - // TODO: allow overriding the state.yaml template - // TODO TODO: if auto.publish == "state", add output_state as an argument - def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml' - def yamlFilename = yamlTemplate - .replaceAll('\\$id', id_) - .replaceAll('\\$\\{id\\}', id_) - .replaceAll('\\$key', key_) - .replaceAll('\\$\\{key\\}', key_) - def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent() - - // the processed state is a list of [key, value, inputPath, outputFilename] tuples, where - // - key is a String - // - value is any object that can be serialized to a Yaml (so a String/Integer/Long/Double/Boolean, a List, a Map, or a Path) - // - inputPath is a List[Path] - // - outputFilename is a List[String] - // - (key, value) are the tuples that will be saved to the state.yaml file - // - (inputPath, outputFilename) are the files that will be copied from src to dest (relative to the state.yaml) - def processedState = - config.allArguments - .findAll { it.direction == "output" } - .collectMany { par -> - def plainName_ = par.plainName - // if the state does not contain the key, it's an - // optional argument for which the component did - // not generate any output - if (!state_.containsKey(plainName_)) { - return [] - } - def value = state_[plainName_] - // if the parameter is not a file, it should be stored - // in the state as-is, but is not something that needs - // to be copied from the source path to the dest path - if (par.type != "file") { - return [[key: plainName_, value: value, inputPath: [], outputFilename: []]] - } - // if the orig state does not contain this filename, - // it's an optional argument for which the user specified - // that it should not be returned as a state - if (!origState_.containsKey(plainName_)) { - return [] - } - def filenameTemplate = origState_[plainName_] - // if the pararameter is multiple: true, fetch the template - if (par.multiple && filenameTemplate instanceof List) { - filenameTemplate = filenameTemplate[0] - } - // instantiate the template - def filename = filenameTemplate - .replaceAll('\\$id', id_) - .replaceAll('\\$\\{id\\}', id_) - .replaceAll('\\$key', key_) - .replaceAll('\\$\\{key\\}', key_) - if (par.multiple) { - // if the parameter is multiple: true, the filename - // should contain a wildcard '*' that is replaced with - // the index of the file - assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}" - def outputPerFile = value.withIndex().collect{ val, ix -> - def filename_ix = filename.replace("*", ix.toString()) - def value_ = java.nio.file.Paths.get(filename_ix) - // if id contains a slash - if (yamlDir != null) { - value_ = yamlDir.relativize(value_) - } - def inputPath = val instanceof File ? val.toPath() : val - [value: value_, inputPath: inputPath, outputFilename: filename_ix] - } - def transposedOutputs = ["value", "inputPath", "outputFilename"].collectEntries{ key -> - [key, outputPerFile.collect{dic -> dic[key]}] - } - return [[key: plainName_] + transposedOutputs] - } else { - def value_ = java.nio.file.Paths.get(filename) - // if id contains a slash - if (yamlDir != null) { - value_ = yamlDir.relativize(value_) - } - def inputPath = value instanceof File ? value.toPath() : value - return [[key: plainName_, value: value_, inputPath: [inputPath], outputFilename: [filename]]] - } - } - - def updatedState_ = processedState.collectEntries{[it.key, it.value]} - def inputPaths = processedState.collectMany{it.inputPath} - def outputFilenames = processedState.collectMany{it.outputFilename} - - // convert state to yaml blob - def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_) - - [id_, yamlBlob_, yamlFilename, inputPaths, outputFilenames] - } - | publishStatesProc - emit: input_ch - } - return publishStatesSimpleWf -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/states/setState.nf' -def setState(fun) { - assert fun instanceof Closure || fun instanceof Map || fun instanceof List : - "Error in setState: Expected process argument to be a Closure, a Map, or a List. Found: class ${fun.getClass()}" - - // if fun is a List, convert to map - if (fun instanceof List) { - // check whether fun is a list[string] - assert fun.every{it instanceof CharSequence} : "Error in setState: argument is a List, but not all elements are Strings" - fun = fun.collectEntries{[it, it]} - } - - // if fun is a map, convert to closure - if (fun instanceof Map) { - // check whether fun is a map[string, string] - assert fun.values().every{it instanceof CharSequence} : "Error in setState: argument is a Map, but not all values are Strings" - assert fun.keySet().every{it instanceof CharSequence} : "Error in setState: argument is a Map, but not all keys are Strings" - def funMap = fun.clone() - // turn the map into a closure to be used later on - fun = { id_, state_ -> - assert state_ instanceof Map : "Error in setState: the state is not a Map" - funMap.collectMany{newkey, origkey -> - if (state_.containsKey(origkey)) { - [[newkey, state_[origkey]]] - } else { - [] - } - }.collectEntries() - } - } - - map { tup -> - def id = tup[0] - def state = tup[1] - def unfilteredState = fun(id, state) - def newState = unfilteredState.findAll{key, val -> val != null} - [id, newState] + tup.drop(2) - } -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/processAuto.nf' -// TODO: unit test processAuto -def processAuto(Map auto) { - // remove null values - auto = auto.findAll{k, v -> v != null} - - // check for unexpected keys - def expectedKeys = ["simplifyInput", "simplifyOutput", "transcript", "publish"] - def unexpectedKeys = auto.keySet() - expectedKeys - assert unexpectedKeys.isEmpty(), "unexpected keys in auto: '${unexpectedKeys.join("', '")}'" - - // check auto.simplifyInput - assert auto.simplifyInput instanceof Boolean, "auto.simplifyInput must be a boolean" - - // check auto.simplifyOutput - assert auto.simplifyOutput instanceof Boolean, "auto.simplifyOutput must be a boolean" - - // check auto.transcript - assert auto.transcript instanceof Boolean, "auto.transcript must be a boolean" - - // check auto.publish - assert auto.publish instanceof Boolean || auto.publish == "state", "auto.publish must be a boolean or 'state'" - - return auto.subMap(expectedKeys) -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/processDirectives.nf' -def assertMapKeys(map, expectedKeys, requiredKeys, mapName) { - assert map instanceof Map : "Expected argument '$mapName' to be a Map. Found: class ${map.getClass()}" - map.forEach { key, val -> - assert key in expectedKeys : "Unexpected key '$key' in ${mapName ? mapName + " " : ""}map" - } - requiredKeys.forEach { requiredKey -> - assert map.containsKey(requiredKey) : "Missing required key '$key' in ${mapName ? mapName + " " : ""}map" - } -} - -// TODO: unit test processDirectives -def processDirectives(Map drctv) { - // remove null values - drctv = drctv.findAll{k, v -> v != null} - - // check for unexpected keys - def expectedKeys = [ - "accelerator", "afterScript", "beforeScript", "cache", "conda", "container", "containerOptions", "cpus", "disk", "echo", "errorStrategy", "executor", "machineType", "maxErrors", "maxForks", "maxRetries", "memory", "module", "penv", "pod", "publishDir", "queue", "label", "scratch", "storeDir", "stageInMode", "stageOutMode", "tag", "time" - ] - def unexpectedKeys = drctv.keySet() - expectedKeys - assert unexpectedKeys.isEmpty() : "Unexpected keys in process directive: '${unexpectedKeys.join("', '")}'" - - /* DIRECTIVE accelerator - accepted examples: - - [ limit: 4, type: "nvidia-tesla-k80" ] - */ - if (drctv.containsKey("accelerator")) { - assertMapKeys(drctv["accelerator"], ["type", "limit", "request", "runtime"], [], "accelerator") - } - - /* DIRECTIVE afterScript - accepted examples: - - "source /cluster/bin/cleanup" - */ - if (drctv.containsKey("afterScript")) { - assert drctv["afterScript"] instanceof CharSequence - } - - /* DIRECTIVE beforeScript - accepted examples: - - "source /cluster/bin/setup" - */ - if (drctv.containsKey("beforeScript")) { - assert drctv["beforeScript"] instanceof CharSequence - } - - /* DIRECTIVE cache - accepted examples: - - true - - false - - "deep" - - "lenient" - */ - if (drctv.containsKey("cache")) { - assert drctv["cache"] instanceof CharSequence || drctv["cache"] instanceof Boolean - if (drctv["cache"] instanceof CharSequence) { - assert drctv["cache"] in ["deep", "lenient"] : "Unexpected value for cache" - } - } - - /* DIRECTIVE conda - accepted examples: - - "bwa=0.7.15" - - "bwa=0.7.15 fastqc=0.11.5" - - ["bwa=0.7.15", "fastqc=0.11.5"] - */ - if (drctv.containsKey("conda")) { - if (drctv["conda"] instanceof List) { - drctv["conda"] = drctv["conda"].join(" ") - } - assert drctv["conda"] instanceof CharSequence - } - - /* DIRECTIVE container - accepted examples: - - "foo/bar:tag" - - [ registry: "reg", image: "im", tag: "ta" ] - is transformed to "reg/im:ta" - - [ image: "im" ] - is transformed to "im:latest" - */ - if (drctv.containsKey("container")) { - assert drctv["container"] instanceof Map || drctv["container"] instanceof CharSequence - if (drctv["container"] instanceof Map) { - def m = drctv["container"] - assertMapKeys(m, [ "registry", "image", "tag" ], ["image"], "container") - def part1 = - System.getenv('OVERRIDE_CONTAINER_REGISTRY') ? System.getenv('OVERRIDE_CONTAINER_REGISTRY') + "/" : - params.containsKey("override_container_registry") ? params["override_container_registry"] + "/" : // todo: remove? - m.registry ? m.registry + "/" : - "" - def part2 = m.image - def part3 = m.tag ? ":" + m.tag : ":latest" - drctv["container"] = part1 + part2 + part3 - } - } - - /* DIRECTIVE containerOptions - accepted examples: - - "--foo bar" - - ["--foo bar", "-f b"] - */ - if (drctv.containsKey("containerOptions")) { - if (drctv["containerOptions"] instanceof List) { - drctv["containerOptions"] = drctv["containerOptions"].join(" ") - } - assert drctv["containerOptions"] instanceof CharSequence - } - - /* DIRECTIVE cpus - accepted examples: - - 1 - - 10 - */ - if (drctv.containsKey("cpus")) { - assert drctv["cpus"] instanceof Integer - } - - /* DIRECTIVE disk - accepted examples: - - "1 GB" - - "2TB" - - "3.2KB" - - "10.B" - */ - if (drctv.containsKey("disk")) { - assert drctv["disk"] instanceof CharSequence - // assert drctv["disk"].matches("[0-9]+(\\.[0-9]*)? *[KMGTPEZY]?B") - // ^ does not allow closures - } - - /* DIRECTIVE echo - accepted examples: - - true - - false - */ - if (drctv.containsKey("echo")) { - assert drctv["echo"] instanceof Boolean - } - - /* DIRECTIVE errorStrategy - accepted examples: - - "terminate" - - "finish" - */ - if (drctv.containsKey("errorStrategy")) { - assert drctv["errorStrategy"] instanceof CharSequence - assert drctv["errorStrategy"] in ["terminate", "finish", "ignore", "retry"] : "Unexpected value for errorStrategy" - } - - /* DIRECTIVE executor - accepted examples: - - "local" - - "sge" - */ - if (drctv.containsKey("executor")) { - assert drctv["executor"] instanceof CharSequence - assert drctv["executor"] in ["local", "sge", "uge", "lsf", "slurm", "pbs", "pbspro", "moab", "condor", "nqsii", "ignite", "k8s", "awsbatch", "google-pipelines"] : "Unexpected value for executor" - } - - /* DIRECTIVE machineType - accepted examples: - - "n1-highmem-8" - */ - if (drctv.containsKey("machineType")) { - assert drctv["machineType"] instanceof CharSequence - } - - /* DIRECTIVE maxErrors - accepted examples: - - 1 - - 3 - */ - if (drctv.containsKey("maxErrors")) { - assert drctv["maxErrors"] instanceof Integer - } - - /* DIRECTIVE maxForks - accepted examples: - - 1 - - 3 - */ - if (drctv.containsKey("maxForks")) { - assert drctv["maxForks"] instanceof Integer - } - - /* DIRECTIVE maxRetries - accepted examples: - - 1 - - 3 - */ - if (drctv.containsKey("maxRetries")) { - assert drctv["maxRetries"] instanceof Integer - } - - /* DIRECTIVE memory - accepted examples: - - "1 GB" - - "2TB" - - "3.2KB" - - "10.B" - */ - if (drctv.containsKey("memory")) { - assert drctv["memory"] instanceof CharSequence - // assert drctv["memory"].matches("[0-9]+(\\.[0-9]*)? *[KMGTPEZY]?B") - // ^ does not allow closures - } - - /* DIRECTIVE module - accepted examples: - - "ncbi-blast/2.2.27" - - "ncbi-blast/2.2.27:t_coffee/10.0" - - ["ncbi-blast/2.2.27", "t_coffee/10.0"] - */ - if (drctv.containsKey("module")) { - if (drctv["module"] instanceof List) { - drctv["module"] = drctv["module"].join(":") - } - assert drctv["module"] instanceof CharSequence - } - - /* DIRECTIVE penv - accepted examples: - - "smp" - */ - if (drctv.containsKey("penv")) { - assert drctv["penv"] instanceof CharSequence - } - - /* DIRECTIVE pod - accepted examples: - - [ label: "key", value: "val" ] - - [ annotation: "key", value: "val" ] - - [ env: "key", value: "val" ] - - [ [label: "l", value: "v"], [env: "e", value: "v"]] - */ - if (drctv.containsKey("pod")) { - if (drctv["pod"] instanceof Map) { - drctv["pod"] = [ drctv["pod"] ] - } - assert drctv["pod"] instanceof List - drctv["pod"].forEach { pod -> - assert pod instanceof Map - // TODO: should more checks be added? - // See https://www.nextflow.io/docs/latest/process.html?highlight=directives#pod - // e.g. does it contain 'label' and 'value', or 'annotation' and 'value', or ...? - } - } - - /* DIRECTIVE publishDir - accepted examples: - - [] - - [ [ path: "foo", enabled: true ], [ path: "bar", enabled: false ] ] - - "/path/to/dir" - is transformed to [[ path: "/path/to/dir" ]] - - [ path: "/path/to/dir", mode: "cache" ] - is transformed to [[ path: "/path/to/dir", mode: "cache" ]] - */ - // TODO: should we also look at params["publishDir"]? - if (drctv.containsKey("publishDir")) { - def pblsh = drctv["publishDir"] - - // check different options - assert pblsh instanceof List || pblsh instanceof Map || pblsh instanceof CharSequence - - // turn into list if not already so - // for some reason, 'if (!pblsh instanceof List) pblsh = [ pblsh ]' doesn't work. - pblsh = pblsh instanceof List ? pblsh : [ pblsh ] - - // check elements of publishDir - pblsh = pblsh.collect{ elem -> - // turn into map if not already so - elem = elem instanceof CharSequence ? [ path: elem ] : elem - - // check types and keys - assert elem instanceof Map : "Expected publish argument '$elem' to be a String or a Map. Found: class ${elem.getClass()}" - assertMapKeys(elem, [ "path", "mode", "overwrite", "pattern", "saveAs", "enabled" ], ["path"], "publishDir") - - // check elements in map - assert elem.containsKey("path") - assert elem["path"] instanceof CharSequence - if (elem.containsKey("mode")) { - assert elem["mode"] instanceof CharSequence - assert elem["mode"] in [ "symlink", "rellink", "link", "copy", "copyNoFollow", "move" ] - } - if (elem.containsKey("overwrite")) { - assert elem["overwrite"] instanceof Boolean - } - if (elem.containsKey("pattern")) { - assert elem["pattern"] instanceof CharSequence - } - if (elem.containsKey("saveAs")) { - assert elem["saveAs"] instanceof CharSequence //: "saveAs as a Closure is currently not supported. Surround your closure with single quotes to get the desired effect. Example: '\{ foo \}'" - } - if (elem.containsKey("enabled")) { - assert elem["enabled"] instanceof Boolean - } - - // return final result - elem - } - // store final directive - drctv["publishDir"] = pblsh - } - - /* DIRECTIVE queue - accepted examples: - - "long" - - "short,long" - - ["short", "long"] - */ - if (drctv.containsKey("queue")) { - if (drctv["queue"] instanceof List) { - drctv["queue"] = drctv["queue"].join(",") - } - assert drctv["queue"] instanceof CharSequence - } - - /* DIRECTIVE label - accepted examples: - - "big_mem" - - "big_cpu" - - ["big_mem", "big_cpu"] - */ - if (drctv.containsKey("label")) { - if (drctv["label"] instanceof CharSequence) { - drctv["label"] = [ drctv["label"] ] - } - assert drctv["label"] instanceof List - drctv["label"].forEach { label -> - assert label instanceof CharSequence - // assert label.matches("[a-zA-Z0-9]([a-zA-Z0-9_]*[a-zA-Z0-9])?") - // ^ does not allow closures - } - } - - /* DIRECTIVE scratch - accepted examples: - - true - - "/path/to/scratch" - - '$MY_PATH_TO_SCRATCH' - - "ram-disk" - */ - if (drctv.containsKey("scratch")) { - assert drctv["scratch"] == true || drctv["scratch"] instanceof CharSequence - } - - /* DIRECTIVE storeDir - accepted examples: - - "/path/to/storeDir" - */ - if (drctv.containsKey("storeDir")) { - assert drctv["storeDir"] instanceof CharSequence - } - - /* DIRECTIVE stageInMode - accepted examples: - - "copy" - - "link" - */ - if (drctv.containsKey("stageInMode")) { - assert drctv["stageInMode"] instanceof CharSequence - assert drctv["stageInMode"] in ["copy", "link", "symlink", "rellink"] - } - - /* DIRECTIVE stageOutMode - accepted examples: - - "copy" - - "link" - */ - if (drctv.containsKey("stageOutMode")) { - assert drctv["stageOutMode"] instanceof CharSequence - assert drctv["stageOutMode"] in ["copy", "move", "rsync"] - } - - /* DIRECTIVE tag - accepted examples: - - "foo" - - '$id' - */ - if (drctv.containsKey("tag")) { - assert drctv["tag"] instanceof CharSequence - } - - /* DIRECTIVE time - accepted examples: - - "1h" - - "2days" - - "1day 6hours 3minutes 30seconds" - */ - if (drctv.containsKey("time")) { - assert drctv["time"] instanceof CharSequence - // todo: validation regex? - } - - return drctv -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/processWorkflowArgs.nf' -def processWorkflowArgs(Map args, Map defaultWfArgs, Map meta) { - // override defaults with args - def workflowArgs = defaultWfArgs + args - - // check whether 'key' exists - assert workflowArgs.containsKey("key") : "Error in module '${meta.config.name}': key is a required argument" - - // if 'key' is a closure, apply it to the original key - if (workflowArgs["key"] instanceof Closure) { - workflowArgs["key"] = workflowArgs["key"](meta.config.name) - } - def key = workflowArgs["key"] - assert key instanceof CharSequence : "Expected process argument 'key' to be a String. Found: class ${key.getClass()}" - assert key ==~ /^[a-zA-Z_]\w*$/ : "Error in module '$key': Expected process argument 'key' to consist of only letters, digits or underscores. Found: ${key}" - - // check for any unexpected keys - def expectedKeys = ["key", "directives", "auto", "map", "mapId", "mapData", "mapPassthrough", "filter", "runIf", "fromState", "toState", "args", "renameKeys", "debug"] - def unexpectedKeys = workflowArgs.keySet() - expectedKeys - assert unexpectedKeys.isEmpty() : "Error in module '$key': unexpected arguments to the '.run()' function: '${unexpectedKeys.join("', '")}'" - - // check whether directives exists and apply defaults - assert workflowArgs.containsKey("directives") : "Error in module '$key': directives is a required argument" - assert workflowArgs["directives"] instanceof Map : "Error in module '$key': Expected process argument 'directives' to be a Map. Found: class ${workflowArgs['directives'].getClass()}" - workflowArgs["directives"] = processDirectives(defaultWfArgs.directives + workflowArgs["directives"]) - - // check whether directives exists and apply defaults - assert workflowArgs.containsKey("auto") : "Error in module '$key': auto is a required argument" - assert workflowArgs["auto"] instanceof Map : "Error in module '$key': Expected process argument 'auto' to be a Map. Found: class ${workflowArgs['auto'].getClass()}" - workflowArgs["auto"] = processAuto(defaultWfArgs.auto + workflowArgs["auto"]) - - // auto define publish, if so desired - if (workflowArgs.auto.publish == true && (workflowArgs.directives.publishDir != null ? workflowArgs.directives.publishDir : [:]).isEmpty()) { - // can't assert at this level thanks to the no_publish profile - // assert params.containsKey("publishDir") || params.containsKey("publish_dir") : - // "Error in module '${workflowArgs['key']}': if auto.publish is true, params.publish_dir needs to be defined.\n" + - // " Example: params.publish_dir = \"./output/\"" - def publishDir = getPublishDir() - - if (publishDir != null) { - workflowArgs.directives.publishDir = [[ - path: publishDir, - saveAs: "{ it.startsWith('.') ? null : it }", // don't publish hidden files, by default - mode: "copy" - ]] - } - } - - // auto define transcript, if so desired - if (workflowArgs.auto.transcript == true) { - // can't assert at this level thanks to the no_publish profile - // assert params.containsKey("transcriptsDir") || params.containsKey("transcripts_dir") || params.containsKey("publishDir") || params.containsKey("publish_dir") : - // "Error in module '${workflowArgs['key']}': if auto.transcript is true, either params.transcripts_dir or params.publish_dir needs to be defined.\n" + - // " Example: params.transcripts_dir = \"./transcripts/\"" - def transcriptsDir = - params.containsKey("transcripts_dir") ? params.transcripts_dir : - params.containsKey("transcriptsDir") ? params.transcriptsDir : - params.containsKey("publish_dir") ? params.publish_dir + "/_transcripts" : - params.containsKey("publishDir") ? params.publishDir + "/_transcripts" : - null - if (transcriptsDir != null) { - def timestamp = nextflow.Nextflow.getSession().getWorkflowMetadata().start.format('yyyy-MM-dd_HH-mm-ss') - def transcriptsPublishDir = [ - path: "$transcriptsDir/$timestamp/\${task.process.replaceAll(':', '-')}/\${id}/", - saveAs: "{ it.startsWith('.') ? it.replaceAll('^.', '') : null }", - mode: "copy" - ] - def publishDirs = workflowArgs.directives.publishDir != null ? workflowArgs.directives.publishDir : null ? workflowArgs.directives.publishDir : [] - workflowArgs.directives.publishDir = publishDirs + transcriptsPublishDir - } - } - - // if this is a stubrun, remove certain directives? - if (workflow.stubRun) { - workflowArgs.directives.keySet().removeAll(["publishDir", "cpus", "memory", "label"]) - } - - for (nam in ["map", "mapId", "mapData", "mapPassthrough", "filter", "runIf"]) { - if (workflowArgs.containsKey(nam) && workflowArgs[nam]) { - assert workflowArgs[nam] instanceof Closure : "Error in module '$key': Expected process argument '$nam' to be null or a Closure. Found: class ${workflowArgs[nam].getClass()}" - } - } - - // TODO: should functions like 'map', 'mapId', 'mapData', 'mapPassthrough' be deprecated as well? - for (nam in ["map", "mapData", "mapPassthrough", "renameKeys"]) { - if (workflowArgs.containsKey(nam) && workflowArgs[nam] != null) { - log.warn "module '$key': workflow argument '$nam' is deprecated and will be removed in Viash 0.9.0. Please use 'fromState' and 'toState' instead." - } - } - - // check fromState - workflowArgs["fromState"] = _processFromState(workflowArgs.get("fromState"), key, meta.config) - - // check toState - workflowArgs["toState"] = _processToState(workflowArgs.get("toState"), key, meta.config) - - // return output - return workflowArgs -} - -def _processFromState(fromState, key_, config_) { - assert fromState == null || fromState instanceof Closure || fromState instanceof Map || fromState instanceof List : - "Error in module '$key_': Expected process argument 'fromState' to be null, a Closure, a Map, or a List. Found: class ${fromState.getClass()}" - if (fromState == null) { - return null - } - - // if fromState is a List, convert to map - if (fromState instanceof List) { - // check whether fromstate is a list[string] - assert fromState.every{it instanceof CharSequence} : "Error in module '$key_': fromState is a List, but not all elements are Strings" - fromState = fromState.collectEntries{[it, it]} - } - - // if fromState is a map, convert to closure - if (fromState instanceof Map) { - // check whether fromstate is a map[string, string] - assert fromState.values().every{it instanceof CharSequence} : "Error in module '$key_': fromState is a Map, but not all values are Strings" - assert fromState.keySet().every{it instanceof CharSequence} : "Error in module '$key_': fromState is a Map, but not all keys are Strings" - def fromStateMap = fromState.clone() - def requiredInputNames = meta.config.allArguments.findAll{it.required && it.direction == "Input"}.collect{it.plainName} - // turn the map into a closure to be used later on - fromState = { it -> - def state = it[1] - assert state instanceof Map : "Error in module '$key_': the state is not a Map" - def data = fromStateMap.collectMany{newkey, origkey -> - // check whether newkey corresponds to a required argument - if (state.containsKey(origkey)) { - [[newkey, state[origkey]]] - } else if (!requiredInputNames.contains(origkey)) { - [] - } else { - throw new Exception("Error in module '$key_': fromState key '$origkey' not found in current state") - } - }.collectEntries() - data - } - } - - return fromState -} - -def _processToState(toState, key_, config_) { - if (toState == null) { - toState = { tup -> tup[1] } - } - - // toState should be a closure, map[string, string], or list[string] - assert toState instanceof Closure || toState instanceof Map || toState instanceof List : - "Error in module '$key_': Expected process argument 'toState' to be a Closure, a Map, or a List. Found: class ${toState.getClass()}" - - // if toState is a List, convert to map - if (toState instanceof List) { - // check whether toState is a list[string] - assert toState.every{it instanceof CharSequence} : "Error in module '$key_': toState is a List, but not all elements are Strings" - toState = toState.collectEntries{[it, it]} - } - - // if toState is a map, convert to closure - if (toState instanceof Map) { - // check whether toState is a map[string, string] - assert toState.values().every{it instanceof CharSequence} : "Error in module '$key_': toState is a Map, but not all values are Strings" - assert toState.keySet().every{it instanceof CharSequence} : "Error in module '$key_': toState is a Map, but not all keys are Strings" - def toStateMap = toState.clone() - def requiredOutputNames = config_.allArguments.findAll{it.required && it.direction == "Output"}.collect{it.plainName} - // turn the map into a closure to be used later on - toState = { it -> - def output = it[1] - def state = it[2] - assert output instanceof Map : "Error in module '$key_': the output is not a Map" - assert state instanceof Map : "Error in module '$key_': the state is not a Map" - def extraEntries = toStateMap.collectMany{newkey, origkey -> - // check whether newkey corresponds to a required argument - if (output.containsKey(origkey)) { - [[newkey, output[origkey]]] - } else if (!requiredOutputNames.contains(origkey)) { - [] - } else { - throw new Exception("Error in module '$key_': toState key '$origkey' not found in current output") - } - }.collectEntries() - state + extraEntries - } - } - - return toState -} - -// helper file: 'src/main/resources/io/viash/runners/nextflow/workflowFactory/workflowFactory.nf' -def _debug(workflowArgs, debugKey) { - if (workflowArgs.debug) { - view { "process '${workflowArgs.key}' $debugKey tuple: $it" } - } else { - map { it } - } -} - -// depends on: innerWorkflowFactory -def workflowFactory(Map args, Map defaultWfArgs, Map meta) { - def workflowArgs = processWorkflowArgs(args, defaultWfArgs, meta) - def key_ = workflowArgs["key"] - - workflow workflowInstance { - take: input_ - - main: - def chModified = input_ - | checkUniqueIds([:]) - | _debug(workflowArgs, "input") - | map { tuple -> - tuple = deepClone(tuple) - - if (workflowArgs.map) { - tuple = workflowArgs.map(tuple) - } - if (workflowArgs.mapId) { - tuple[0] = workflowArgs.mapId(tuple[0]) - } - if (workflowArgs.mapData) { - tuple[1] = workflowArgs.mapData(tuple[1]) - } - if (workflowArgs.mapPassthrough) { - tuple = tuple.take(2) + workflowArgs.mapPassthrough(tuple.drop(2)) - } - - // check tuple - assert tuple instanceof List : - "Error in module '${key_}': element in channel should be a tuple [id, data, ...otherargs...]\n" + - " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + - " Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}" - assert tuple.size() >= 2 : - "Error in module '${key_}': expected length of tuple in input channel to be two or greater.\n" + - " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + - " Found: tuple.size() == ${tuple.size()}" - - // check id field - if (tuple[0] instanceof GString) { - tuple[0] = tuple[0].toString() - } - assert tuple[0] instanceof CharSequence : - "Error in module '${key_}': first element of tuple in channel should be a String\n" + - " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + - " Found: ${tuple[0]}" - - // match file to input file - if (workflowArgs.auto.simplifyInput && (tuple[1] instanceof Path || tuple[1] instanceof List)) { - def inputFiles = meta.config.allArguments - .findAll { it.type == "file" && it.direction == "input" } - - assert inputFiles.size() == 1 : - "Error in module '${key_}' id '${tuple[0]}'.\n" + - " Anonymous file inputs are only allowed when the process has exactly one file input.\n" + - " Expected: inputFiles.size() == 1. Found: inputFiles.size() is ${inputFiles.size()}" - - tuple[1] = [[ inputFiles[0].plainName, tuple[1] ]].collectEntries() - } - - // check data field - assert tuple[1] instanceof Map : - "Error in module '${key_}' id '${tuple[0]}': second element of tuple in channel should be a Map\n" + - " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + - " Expected class: Map. Found: tuple[1].getClass() is ${tuple[1].getClass()}" - - // rename keys of data field in tuple - if (workflowArgs.renameKeys) { - assert workflowArgs.renameKeys instanceof Map : - "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + - " Example: renameKeys: ['new_key': 'old_key'].\n" + - " Expected class: Map. Found: renameKeys.getClass() is ${workflowArgs.renameKeys.getClass()}" - assert tuple[1] instanceof Map : - "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + - " Expected class: Map. Found: tuple[1].getClass() is ${tuple[1].getClass()}" - - // TODO: allow renameKeys to be a function? - workflowArgs.renameKeys.each { newKey, oldKey -> - assert newKey instanceof CharSequence : - "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + - " Example: renameKeys: ['new_key': 'old_key'].\n" + - " Expected class of newKey: String. Found: newKey.getClass() is ${newKey.getClass()}" - assert oldKey instanceof CharSequence : - "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + - " Example: renameKeys: ['new_key': 'old_key'].\n" + - " Expected class of oldKey: String. Found: oldKey.getClass() is ${oldKey.getClass()}" - assert tuple[1].containsKey(oldKey) : - "Error renaming data keys in module '${key}' id '${tuple[0]}'.\n" + - " Key '$oldKey' is missing in the data map. tuple[1].keySet() is '${tuple[1].keySet()}'" - tuple[1].put(newKey, tuple[1][oldKey]) - } - tuple[1].keySet().removeAll(workflowArgs.renameKeys.collect{ newKey, oldKey -> oldKey }) - } - tuple - } - - - def chRun = null - def chPassthrough = null - if (workflowArgs.runIf) { - def runIfBranch = chModified.branch{ tup -> - run: workflowArgs.runIf(tup[0], tup[1]) - passthrough: true - } - chRun = runIfBranch.run - chPassthrough = runIfBranch.passthrough - } else { - chRun = chModified - chPassthrough = Channel.empty() - } - - def chRunFiltered = workflowArgs.filter ? - chRun | filter{workflowArgs.filter(it)} : - chRun - - def chArgs = workflowArgs.fromState ? - chRunFiltered | map{ - def new_data = workflowArgs.fromState(it.take(2)) - [it[0], new_data] - } : - chRunFiltered | map {tup -> tup.take(2)} - - // fill in defaults - def chArgsWithDefaults = chArgs - | map { tuple -> - def id_ = tuple[0] - def data_ = tuple[1] - - // TODO: could move fromState to here - - // fetch default params from functionality - def defaultArgs = meta.config.allArguments - .findAll { it.containsKey("default") } - .collectEntries { [ it.plainName, it.default ] } - - // fetch overrides in params - def paramArgs = meta.config.allArguments - .findAll { par -> - def argKey = key_ + "__" + par.plainName - params.containsKey(argKey) - } - .collectEntries { [ it.plainName, params[key_ + "__" + it.plainName] ] } - - // fetch overrides in data - def dataArgs = meta.config.allArguments - .findAll { data_.containsKey(it.plainName) } - .collectEntries { [ it.plainName, data_[it.plainName] ] } - - // combine params - def combinedArgs = defaultArgs + paramArgs + workflowArgs.args + dataArgs - - // remove arguments with explicit null values - combinedArgs - .removeAll{_, val -> val == null || val == "viash_no_value" || val == "force_null"} - - combinedArgs = _processInputValues(combinedArgs, meta.config, id_, key_) - - [id_, combinedArgs] + tuple.drop(2) - } - - // TODO: move some of the _meta.join_id wrangling to the safeJoin() function. - def chInitialOutput = chArgsWithDefaults - | _debug(workflowArgs, "processed") - // run workflow - | innerWorkflowFactory(workflowArgs) - // check output tuple - | map { id_, output_ -> - - // see if output map contains metadata - def meta_ = - output_ instanceof Map && output_.containsKey("_meta") ? - output_["_meta"] : - [:] - def join_id = meta_.join_id ?: id_ - - // remove metadata - output_ = output_.findAll{k, v -> k != "_meta"} - - // check value types - output_ = _processOutputValues(output_, meta.config, id_, key_) - - // simplify output if need be - if (workflowArgs.auto.simplifyOutput && output_.size() == 1) { - output_ = output_.values()[0] - } - - [join_id, id_, output_] - } - // | view{"chInitialOutput: ${it.take(3)}"} - - // join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...] - def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_) - // input tuple format: [join_id, id, output, prev_state, ...] - // output tuple format: [join_id, id, new_state, ...] - | map{ tup -> - def new_state = workflowArgs.toState(tup.drop(1).take(3)) - tup.take(2) + [new_state] + tup.drop(4) - } - - if (workflowArgs.auto.publish == "state") { - def chPublish = chNewState - // input tuple format: [join_id, id, new_state, ...] - // output tuple format: [join_id, id, new_state] - | map{ tup -> - tup.take(3) - } - - safeJoin(chPublish, chArgsWithDefaults, key_) - // input tuple format: [join_id, id, new_state, orig_state, ...] - // output tuple format: [id, new_state, orig_state] - | map { tup -> - tup.drop(1).take(3) - } - | publishStatesByConfig(key: key_, config: meta.config) - } - - // remove join_id and meta - chReturn = chNewState - | map { tup -> - // input tuple format: [join_id, id, new_state, ...] - // output tuple format: [id, new_state, ...] - tup.drop(1) - } - | _debug(workflowArgs, "output") - | concat(chPassthrough) - - emit: chReturn - } - - def wf = workflowInstance.cloneWithName(key_) - - // add factory function - wf.metaClass.run = { runArgs -> - workflowFactory(runArgs, workflowArgs, meta) - } - // add config to module for later introspection - wf.metaClass.config = meta.config - - return wf -} - -nextflow.enable.dsl=2 - -// START COMPONENT-SPECIFIC CODE - -// create meta object -meta = [ - "resources_dir": moduleDir.toRealPath().normalize(), - "config": processConfig(readJsonBlob('''{ - "name" : "rnaseq", - "namespace" : "workflows", - "version" : "multiple_fixes", - "argument_groups" : [ - { - "name" : "Input", - "arguments" : [ - { - "type" : "string", - "name" : "--id", - "description" : "ID of the sample.", - "example" : [ - "foo" - ], - "required" : true, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--fastq_1", - "description" : "Path to the sample (or read 1 of paired end sample).", - "must_exist" : true, - "create_parent" : true, - "required" : true, - "direction" : "input", - "multiple" : true, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--fastq_2", - "description" : "Path to read 2 of the sample.", - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : true, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--strandedness", - "description" : "Sample strand-specificity. Must be one of unstranded, forward, reverse or auto", - "default" : [ - "auto" - ], - "required" : false, - "choices" : [ - "unstranded", - "forward", - "reverse", - "auto" - ], - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - } - ] - }, - { - "name" : "Reference genome options", - "arguments" : [ - { - "type" : "file", - "name" : "--fasta", - "description" : "Path to FASTA genome file.", - "must_exist" : true, - "create_parent" : true, - "required" : true, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--gtf", - "description" : "Path to GTF annotation file. This parameter is *mandatory* if --genome is not specified.", - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--gff", - "description" : "Path to GFF3 annotation file. Required if \\"--gtf\\" is not specified.", - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--additional_fasta", - "description" : "FASTA file to concatenate to genome FASTA file e.g. containing spike-in sequences.", - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--transcript_fasta", - "description" : "Path to FASTA transcriptome file.", - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--gene_bed", - "description" : "Path to BED file containing gene intervals. This will be created from the GTF file if not specified.", - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--splicesites", - "description" : "Splice sites file required for HISAT2.", - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--star_index", - "description" : "Path to directory or tar.gz archive for pre-built STAR index.", - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--rsem_index", - "description" : "Path to directory or tar.gz archive for pre-built RSEM index.", - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--salmon_index", - "description" : "Path to directory or tar.gz archive for pre-built Salmon index.", - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--kallisto_index", - "description" : "Path to directory or tar.gz archive for pre-built Kallisto index.", - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "boolean_true", - "name" : "--gencode", - "description" : "Specify if the GTF annotation is in GENCODE format.", - "direction" : "input" - }, - { - "type" : "string", - "name" : "--gtf_extra_attributes", - "description" : "Additional gene identifiers from the input GTF file when running Salmon. More than one value can be specified separated by comma.", - "default" : [ - "gene_name" - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--gtf_group_features", - "description" : "Define the attribute type used to group features in the GTF file when running Salmon.", - "default" : [ - "gene_id" - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--featurecounts_group_type", - "description" : "The attribute type used to group feature types in the GTF file when generating the biotype plot with featureCounts.", - "default" : [ - "gene_biotype" - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--featurecounts_feature_type", - "description" : "By default, the pipeline assigns reads based on the 'exon' attribute within the GTF file.", - "default" : [ - "exon" - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - } - ] - }, - { - "name" : "Read trimming options", - "arguments" : [ - { - "type" : "string", - "name" : "--trimmer", - "description" : "Specify the trimming tool to use.", - "default" : [ - "trimgalore" - ], - "required" : false, - "choices" : [ - "trimgalore", - "fastp" - ], - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--extra_trimgalore_args", - "description" : "Extra arguments to pass to Trim Galore! command in addition to defaults defined by the pipeline.", - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--extra_fastp_args", - "description" : "Extra arguments to pass to fastp command in addition to defaults defined by the pipeline.", - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "integer", - "name" : "--min_trimmed_reads", - "description" : "Minimum number of trimmed reads below which samples are removed from further processing. Some downstream steps in the pipeline will fail if this threshold is too low.", - "default" : [ - 10000 - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - } - ] - }, - { - "name" : "Read filtering options", - "arguments" : [ - { - "type" : "file", - "name" : "--bbsplit_fasta_list", - "description" : "Path to comma-separated file containing a list of reference genomes to filter reads against with BBSplit. To use BBSplit, \\"--skip_bbsplit\\" must be explicitly set to \\"false\\". The file should contain 2 (comma separated) columns - short name and full path to reference genome(s)", - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--bbsplit_index", - "description" : "Path to directory or tar.gz archive for pre-built BBSplit index.", - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "boolean_true", - "name" : "--remove_ribo_rna", - "description" : "Enable the removal of reads derived from ribosomal RNA using SortMeRNA.", - "direction" : "input" - }, - { - "type" : "file", - "name" : "--ribo_database_manifest", - "description" : "Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA.", - "default" : [ - "assets/rrna-db-defaults.txt" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - } - ] - }, - { - "name" : "UMI options", - "arguments" : [ - { - "type" : "boolean_true", - "name" : "--with_umi", - "description" : "Enable UMI-based read deduplication.", - "direction" : "input" - }, - { - "type" : "string", - "name" : "--umitools_extract_method", - "description" : "UMI pattern to use.", - "default" : [ - "string" - ], - "required" : false, - "choices" : [ - "string", - "regex" - ], - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--umitools_bc_pattern", - "description" : "The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the first 6 nucleotides of the read are from the UMI.", - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--umitools_bc_pattern2", - "description" : "The UMI barcode pattern to use if the UMI is located in read 2.", - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "integer", - "name" : "--umi_discard_read", - "description" : "After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively.", - "default" : [ - 0 - ], - "required" : false, - "choices" : [ - 0, - 1, - 2 - ], - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--umitools_umi_separator", - "description" : "The character that separates the UMI in the read name. Most likely a colon if you skipped the extraction with UMI-tools and used other software.", - "default" : [ - "_" - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--umitools_grouping_method", - "description" : "Method to use to determine read groups by subsuming those with similar UMIs. All methods start by identifying the reads with the same mapping position, but treat similar yet nonidentical UMIs differently.", - "default" : [ - "directional" - ], - "required" : false, - "choices" : [ - "unique", - "percentile", - "cluster", - "adjacency", - "directional" - ], - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "boolean_true", - "name" : "--umi_dedup_stats", - "description" : "Generate output stats when running \\"umi_tools dedup\\".", - "direction" : "input" - } - ] - }, - { - "name" : "Alignment options", - "arguments" : [ - { - "type" : "string", - "name" : "--aligner", - "description" : "Specifies the alignment algorithm to use - available options are 'star_salmon', 'star_rsem' and 'hisat2'.", - "default" : [ - "star_salmon" - ], - "required" : false, - "choices" : [ - "star_salmon", - "star_rsem", - "hisat2" - ], - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--pseudo_aligner", - "description" : "Specifies the pseudo aligner to use - available options are 'salmon'. Runs in addition to '--aligner'.", - "default" : [ - "salmon" - ], - "required" : false, - "choices" : [ - "salmon", - "kallisto" - ], - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "integer", - "name" : "--pseudo_aligner_kmer_size", - "description" : "Kmer length passed to indexing step of pseudoaligners.", - "default" : [ - 31 - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "integer", - "name" : "--kallisto_quant_fragment_length", - "description" : "For single-end mode only, the estimated average fragment length to use for quantification with Kallisto.", - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "integer", - "name" : "--kallisto_quant_fragment_length_sd", - "description" : "For single-end mode only, the estimated standard deviation of the fragment length for quantification with Kallisto.", - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "boolean_true", - "name" : "--bam_csi_index", - "description" : "Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes.", - "direction" : "input" - }, - { - "type" : "string", - "name" : "--salmon_quant_libtype", - "description" : "Override Salmon library type inferred based on strandedness defined in meta object.", - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--extra_salmon_quant_args", - "description" : "Extra arguments to pass to salmon quant command in addition to defaults defined by the pipeline.", - "default" : [ - "-v" - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "integer", - "name" : "--min_mapped_reads", - "description" : "Minimum percentage of uniquely mapped reads below which samples are removed from further processing.", - "default" : [ - 5 - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "boolean_true", - "name" : "--stringtie_ignore_gtf", - "description" : "Perform reference-guided de novo assembly of transcripts using StringTie, i.e. don't restrict to those in GTF file.", - "direction" : "input" - }, - { - "type" : "string", - "name" : "--extra_stringtie_args", - "description" : "Extra arguments to pass to stringtie command in addition to defaults defined by the pipeline.", - "default" : [ - "-v" - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "boolean_true", - "name" : "--save_unaligned", - "description" : "Where possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory.", - "direction" : "input" - }, - { - "type" : "boolean_true", - "name" : "--save_align_intermeds", - "description" : "Save the intermediate BAM files from the alignment step.", - "direction" : "input" - }, - { - "type" : "boolean_true", - "name" : "--skip_alignment", - "description" : "Skip all of the alignment-based processes within the pipeline.", - "direction" : "input" - }, - { - "type" : "boolean_true", - "name" : "--skip_pseudo_alignment", - "description" : "Skip all of the pseudo-alignment-based processes within the pipeline.", - "direction" : "input" - }, - { - "type" : "string", - "name" : "--extra_rsem_calculate_expression_args", - "description" : "Extra arguments to pass to rsem-calculate-expression command in addition to defaults defined by the pipeline.", - "default" : [ - "--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1" - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - } - ] - }, - { - "name" : "Process skipping options", - "arguments" : [ - { - "type" : "boolean", - "name" : "--skip_fastqc", - "description" : "Skip FatQC step.", - "default" : [ - false - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "boolean", - "name" : "--skip_trimming", - "description" : "Skip the adapter trimming step.", - "default" : [ - false - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "boolean_true", - "name" : "--skip_bbsplit", - "description" : "Skip BBSplit for removal of non-reference genome reads.", - "direction" : "input" - }, - { - "type" : "boolean", - "name" : "--skip_umi_extract", - "description" : "Skip umi_tools extract step.", - "default" : [ - false - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "boolean_true", - "name" : "--skip_qc", - "description" : "Skip all QC steps except for MultiQC.", - "direction" : "input" - }, - { - "type" : "boolean_true", - "name" : "--skip_markduplicates", - "description" : "Skip picard MarkDuplicates step.", - "direction" : "input" - }, - { - "type" : "boolean_true", - "name" : "--skip_stringtie", - "description" : "Skip StringTie.", - "direction" : "input" - }, - { - "type" : "boolean_true", - "name" : "--skip_biotype_qc", - "description" : "Skip additional featureCounts process for biotype QC.", - "direction" : "input" - }, - { - "type" : "boolean_true", - "name" : "--skip_bigwig", - "description" : "Skip bigWig file creation.", - "direction" : "input" - }, - { - "type" : "boolean_true", - "name" : "--skip_preseq", - "description" : "Skip Preseq.", - "direction" : "input" - }, - { - "type" : "boolean_true", - "name" : "--skip_deseq2_qc", - "description" : "Skip DESeq2 PCA and heatmap plotting.", - "direction" : "input" - }, - { - "type" : "boolean_true", - "name" : "skip_dupradar", - "description" : "Skip dupRadar.", - "direction" : "input" - }, - { - "type" : "boolean_true", - "name" : "skip_rseqc", - "description" : "Skip RSeQC.", - "direction" : "input" - }, - { - "type" : "boolean_true", - "name" : "skip_multiqc", - "description" : "Skip MultiQC.", - "direction" : "input" - } - ] - }, - { - "name" : "Other process arguments", - "arguments" : [ - { - "type" : "string", - "name" : "--extra_fq_subsample_args", - "description" : "Extra arguments to pass to fq subsample command in addition to defaults defined by the pipeline.", - "default" : [ - " --record-count 1000000 --seed 1" - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--extra_picard_args", - "description" : "Extra arguments to pass to picard MarkDuplicates command in addition to defaults defined by the pipeline.", - "default" : [ - " --ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp" - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--extra_bedtools_args", - "description" : "Extra arguments to pass to bedtools genomecov command in addition to defaults defined by the pipeline.", - "default" : [ - " -split -du" - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--extra_featurecounts_args", - "description" : "Extra arguments to pass to featureCounts command in addition to defaults defined by the pipeline", - "default" : [ - " -B -C" - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--extra_preseq_args", - "description" : "Extra arguments to pass to preseq lc_extrap command in addition to defaults defined by the pipeline", - "default" : [ - "-verbose -seed 1 -seg_len 100000000" - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--pca_header_multiqc", - "default" : [ - "assets/multiqc/deseq2_pca_header.txt" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--clustering_header_multiqc", - "default" : [ - "assets/multiqc/deseq2_clustering_header.txt" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "boolean", - "name" : "--deseq2_vst", - "description" : "Use vst transformation instead of rlog with DESeq2", - "default" : [ - true - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--extra_deseq2_args", - "default" : [ - "--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3" - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--extra_deseq2_args2", - "default" : [ - "star_salmon" - ], - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--rseqc_modules", - "description" : "Specify the RSeQC modules to run_wf", - "default" : [ - "bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication" - ], - "required" : false, - "choices" : [ - "bam_stat", - "inner_distance", - "infer_experiment", - "junction_annotation", - "junction_saturation", - "read_distribution", - "read_duplication", - "tin" - ], - "direction" : "input", - "multiple" : true, - "multiple_sep" : "," - } - ] - }, - { - "name" : "Multiqc paramenters", - "arguments" : [ - { - "type" : "file", - "name" : "--multiqc_custom_config", - "default" : [ - "assets/multiqc_config.yml" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "string", - "name" : "--multiqc_title", - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--multiqc_methods_description", - "default" : [ - "assets/methods_description_template.yml" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "input", - "multiple" : false, - "multiple_sep" : ";" - } - ] - }, - { - "name" : "Output", - "arguments" : [ - { - "type" : "file", - "name" : "--output_fasta", - "default" : [ - "genome/reference_genome.fasta" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--output_gtf", - "default" : [ - "genome/gene_annotation.gtf" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--output_transcript_fasta", - "default" : [ - "genome/transcriptome.fasta" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--output_gene_bed", - "default" : [ - "genome/gene_annotation.bed" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--output_star_index", - "description" : "Path to STAR index.", - "default" : [ - "genome/index/STAR" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--output_salmon_index", - "description" : "Path to Salmon index.", - "default" : [ - "genome/index/Salmon" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--output_bbsplit_index", - "description" : "Path to BBSplit index.", - "default" : [ - "genome/index/BBSplit" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--output_kallisto_index", - "description" : "Path to Kallisto index.", - "default" : [ - "genome/index/Kallisto" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--output_fastq_1", - "description" : "Path to output directory", - "default" : [ - "fastq/$id.read_1.fastq" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--output_fastq_2", - "description" : "Path to output directory", - "default" : [ - "fastq/$id.read_2.fastq" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--fastqc_html_1", - "description" : "FastQC HTML report for read 1.", - "default" : [ - "fastqc_raw/$id.read_1.fastqc.html" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--fastqc_html_2", - "description" : "FastQC HTML report for read 2.", - "default" : [ - "fastqc_raw/$id.read_2.fastqc.html" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--fastqc_zip_1", - "description" : "FastQC report archive for read 1.", - "default" : [ - "fastqc_raw/$id.read_1.fastqc.zip" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--fastqc_zip_2", - "description" : "FastQC report archive for read 2.", - "default" : [ - "fastqc_raw/$id.read_2.fastqc.zip" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--trim_log_1", - "default" : [ - "trimgalore/$id.read_1.trimming_report.txt" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--trim_log_2", - "default" : [ - "trimgalore/$id.read_2.trimming_report.txt" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--trim_html_1", - "default" : [ - "fastqc_trim/$id.read_1.trimmed_fastqc.html" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--trim_html_2", - "default" : [ - "fastqc_trim/$id.read_2.trimmed_fastqc.html" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--trim_zip_1", - "default" : [ - "fastqc_trim/$id.read_1.trimmed_fastqc.zip" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--trim_zip_2", - "default" : [ - "fastqc_trim/$id.read_2.trimmed_fastqc.zip" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--sortmerna_log", - "description" : "Sortmerna log file.", - "default" : [ - "sortmerna/$id.log" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--star_alignment", - "default" : [ - "STAR_alignment/$id" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--genome_bam_sorted", - "default" : [ - "STAR_alignment/genome_processed/$id.genome.bam" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--genome_bam_index", - "default" : [ - "STAR_alignment/genome_processed/$id.genome.bam.bai" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--genome_bam_stats", - "default" : [ - "samtools_stats/$id.genome.stats" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--genome_bam_flagstat", - "default" : [ - "samtools_stats/$id.genome.flagstat" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--genome_bam_idxstats", - "default" : [ - "samtools_stats/$id.genome.idxstats" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--transcriptome_bam", - "default" : [ - "STAR_alignment/transcriptome_processed/$id.transcriptome.bam" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--transcriptome_bam_index", - "default" : [ - "STAR_alignment/transcriptome_processed/$id.transcriptome.bam.bai" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--transcriptome_bam_stats", - "default" : [ - "samtools_stats/$id.transcriptome.stats" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--transcriptome_bam_flagstat", - "default" : [ - "samtools_stats/$id.transcriptome.flagstat" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--transcriptome_bam_idxstats", - "default" : [ - "samtools_stats/$id.transcriptome.idxstats" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--salmon_quant_results", - "default" : [ - "salmon/$id" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--tpm_gene", - "default" : [ - "salmon/gene_tpm.tsv" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--counts_gene", - "default" : [ - "salmon/gene_counts.tsv" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--counts_gene_length_scaled", - "default" : [ - "salmon/gene_counts_length_scaled.tsv" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--counts_gene_scaled", - "default" : [ - "salmon/gene_counts_scaled.tsv" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--tpm_transcript", - "default" : [ - "salmon/transcript_tpm.tsv" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--counts_transcript", - "default" : [ - "salmon/transcript_counts.tsv" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--salmon_merged_summarizedexperiment", - "default" : [ - "salmon/summarizedexperiment" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--markduplicates_metrics", - "default" : [ - "picard/$id.sorted.MarkDuplicates.metrics.txt" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--stringtie_transcript_gtf", - "default" : [ - "stringtie/$id.transcripts.gtf" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--stringtie_coverage_gtf", - "default" : [ - "stringtie/$id.coverage.gtf" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--stringtie_abundance", - "default" : [ - "stringtie/$id.gene_abundance.txt" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--stringtie_ballgown", - "default" : [ - "stringtie/$id.ballgown" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--featurecounts", - "default" : [ - "featurecounts/$id.featureCounts.txt" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--featurecounts_summary", - "default" : [ - "featurecounts/$id.featureCounts.txt.summary" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--featurecounts_multiqc", - "default" : [ - "featurecounts/$id.featureCounts_mqc.tsv" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--featurecounts_rrna_multiqc", - "default" : [ - "featurecounts/$id.featureCounts_rrna_mqc.tsv" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--bedgraph_forward", - "default" : [ - "bedgraph/$id.forward.bedgraph" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--bedgraph_reverse", - "default" : [ - "bedgraph/$id.reverse.bedgraph" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--bigwig_forward", - "default" : [ - "bigwig/$id.forward.bigwig" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--bigwig_reverse", - "default" : [ - "bigwig/$id.reverse.bigwig" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--preseq_output", - "default" : [ - "preseq/$id.lc_extrap.txt" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--bamstat_output", - "description" : "Path to output file (txt) of mapping quality statistics", - "default" : [ - "RSeQC/bamstat/$id.mapping_quality.txt" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--strandedness_output", - "description" : "Path to output report (txt) of inferred strandedness", - "default" : [ - "RSeQC/inferexperiment/$id.strandedness.txt" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--inner_dist_output_stats", - "description" : "output file (txt) with summary statistics of inner distances of paired reads", - "default" : [ - "RSeQC/innerdistance/$id.inner_distance.stats" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--inner_dist_output_dist", - "description" : "output file (txt) with inner distances of all paired reads", - "default" : [ - "RSeQC/innerdistance/txt/$id.inner_distance.txt" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--inner_dist_output_freq", - "description" : "output file (txt) with frequencies of inner distances of all paired reads", - "default" : [ - "RSeQC/innerdistance/txt/$id.inner_distance_freq.txt" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--inner_dist_output_plot", - "description" : "output file (pdf) with histogram plot of of inner distances of all paired reads", - "default" : [ - "RSeQC/innerdistance/pdf/$id.inner_distance_plot.pdf" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--inner_dist_output_plot_r", - "description" : "output file (R) with script of histogram plot of of inner distances of all paired reads", - "default" : [ - "RSeQC/innerdistance/rscript/$id.inner_distance_plot.r" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--junction_annotation_output_log", - "description" : "output log of junction annotation script", - "default" : [ - "RSeQC/junctionannotation/log/$id.junction_annotation.log" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--junction_annotation_output_plot_r", - "description" : "R script to generate splice_junction and splice_events plot", - "default" : [ - "RSeQC/junctionannotation/rscript/$id.junction_annotation_plot.r" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--junction_annotation_output_junction_bed", - "description" : "junction annotation file (bed format)", - "default" : [ - "RSeQC/junctionannotation/bed/$id.junction_annotation.bed" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--junction_annotation_output_junction_interact", - "description" : "interact file (bed format) of junctions. Can be uploaded to UCSC genome browser or converted to bigInteract (using bedToBigBed program) for visualization.", - "default" : [ - "RSeQC/junctionannotation/bed/$id.junction_annotation.Interact.bed" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--junction_annotation_output_junction_sheet", - "description" : "junction annotation file (xls format)", - "default" : [ - "RSeQC/junctionannotation/xls/$id.junction_annotation.xls" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--junction_annotation_output_splice_events_plot", - "description" : "plot of splice events (pdf)", - "default" : [ - "RSeQC/junctionannotation/pdf/$id.splice_events.pdf" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--junction_annotation_output_splice_junctions_plot", - "description" : "plot of junctions (pdf)", - "default" : [ - "RSeQC/junctionannotation/pdf/$id.splice_junctions_plot.pdf" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--junction_saturation_output_plot_r", - "description" : "r script to generate junction_saturation_plot plot", - "default" : [ - "RSeQC/junctionsaturation/rscript/$id.junction_saturation_plot.r" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--junction_saturation_output_plot", - "description" : "plot of junction saturation (pdf", - "default" : [ - "RSeQC/junctionsaturation/pdf/$id.junction_saturation_plot.pdf" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--read_distribution_output", - "description" : "output file (txt) of read distribution analysis.", - "default" : [ - "RSeQC/readdistribution/$id.read_distribution.txt" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--read_duplication_output_duplication_rate_plot_r", - "description" : "R script for generating duplication rate plot", - "default" : [ - "RSeQC/readduplication/rscrpt/$id.duplication_rate_plot.r" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--read_duplication_output_duplication_rate_plot", - "description" : "duplication rate plot (pdf)", - "default" : [ - "RSeQC/readduplication/pdf/$id.duplication_rate_plot.pdf" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--read_duplication_output_duplication_rate_mapping", - "description" : "Summary of mapping-based read duplication", - "default" : [ - "RSeQC/readduplication/xls/$id.duplication_rate_mapping.xls" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--read_duplication_output_duplication_rate_sequence", - "description" : "Summary of sequencing-based read duplication", - "default" : [ - "RSeQC/readduplication/xls/$id.duplication_rate_sequencing.xls" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--tin_output_summary", - "description" : "summary statistics (txt) of calculated TIN metrics", - "default" : [ - "RSeQC/tin/txt/$id.tin_summary.txt" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--tin_output_metrics", - "description" : "file with TIN metrics (xls)", - "default" : [ - "RSeQC/tin/xls/$id.tin.xls" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--dupradar_output_dupmatrix", - "description" : "path to output file (txt) of duplicate tag counts", - "default" : [ - "dupradar/gene_data/$id.dup_matrix.txt" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--dupradar_output_dup_intercept_mqc", - "description" : "path to output file (txt) of multiqc intercept value DupRadar", - "default" : [ - "dupradar/mqc_intercept/$id.dup_intercept_mqc.txt" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--dupradar_output_duprate_exp_boxplot", - "description" : "path to output file (pdf) of distribution of expression box plot", - "default" : [ - "dupradar/box_plot/$id.duprate_exp_boxplot.pdf" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--dupradar_output_duprate_exp_densplot", - "description" : "path to output file (pdf) of 2D density scatter plot of duplicate tag counts", - "default" : [ - "dupradar/scatter_plot/$id.duprate_exp_densityplot.pdf" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--dupradar_output_duprate_exp_denscurve_mqc", - "description" : "path to output file (pdf) of density curve of gene duplication multiqc", - "default" : [ - "dupradar/density_curve/$id.duprate_exp_density_curve_mqc.pdf" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--dupradar_output_expression_histogram", - "description" : "path to output file (pdf) of distribution of RPK values per gene histogram", - "default" : [ - "dupradar/histogram/$id.expression_hist.pdf" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--dupradar_output_intercept_slope", - "default" : [ - "dupradar/intercept_slope/$id.intercept_slope.txt" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--qualimap_output_pdf", - "default" : [ - "qualimap/$id.qualimap_output.pdf" - ], - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--qualimap_output_dir", - "default" : [ - "qualimap/$id" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--deseq2_output", - "default" : [ - "deseq2_qc" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--multiqc_report", - "default" : [ - "multiqc/multiqc_report.html" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--multiqc_data", - "default" : [ - "multiqc/multiqc_data" - ], - ''' + ''' "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--multiqc_plots", - "default" : [ - "multiqc/multiqc_plots" - ], - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--multiqc_versions", - "must_exist" : true, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - }, - { - "type" : "file", - "name" : "--versions", - "must_exist" : false, - "create_parent" : true, - "required" : false, - "direction" : "output", - "multiple" : false, - "multiple_sep" : ";" - } - ] - } - ], - "resources" : [ - { - "type" : "nextflow_script", - "path" : "main.nf", - "is_executable" : true, - "entrypoint" : "run_wf" - } - ], - "description" : "A viash workflow for the nf-core/rnaseq pipeline.\n", - "status" : "enabled", - "requirements" : { - "commands" : [ - "ps" - ] - }, - "dependencies" : [ - { - "name" : "workflows/prepare_genome", - "repository" : { - "type" : "local" - } - }, - { - "name" : "cat_fastq", - "repository" : { - "type" : "local" - } - }, - { - "name" : "workflows/pre_processing", - "repository" : { - "type" : "local" - } - }, - { - "name" : "workflows/genome_alignment_and_quant", - "repository" : { - "type" : "local" - } - }, - { - "name" : "workflows/pseudo_alignment_and_quant", - "repository" : { - "type" : "local" - } - }, - { - "name" : "workflows/post_processing", - "repository" : { - "type" : "local" - } - }, - { - "name" : "workflows/quality_control", - "repository" : { - "type" : "local" - } - } - ], - "repositories" : [ - { - "type" : "vsh", - "name" : "biobox", - "repo" : "vsh/biobox", - "tag" : "v0.2.0" - }, - { - "type" : "vsh", - "name" : "craftbox", - "repo" : "craftbox", - "tag" : "v0.1.0" - } - ], - "runners" : [ - { - "type" : "executable", - "id" : "executable", - "docker_setup_strategy" : "ifneedbepullelsecachedbuild" - }, - { - "type" : "nextflow", - "id" : "nextflow", - "directives" : { - "tag" : "$id" - }, - "auto" : { - "simplifyInput" : true, - "simplifyOutput" : false, - "transcript" : false, - "publish" : false - }, - "config" : { - "labels" : { - "mem1gb" : "memory = 1000000000.B", - "mem2gb" : "memory = 2000000000.B", - "mem5gb" : "memory = 5000000000.B", - "mem10gb" : "memory = 10000000000.B", - "mem20gb" : "memory = 20000000000.B", - "mem50gb" : "memory = 50000000000.B", - "mem100gb" : "memory = 100000000000.B", - "mem200gb" : "memory = 200000000000.B", - "mem500gb" : "memory = 500000000000.B", - "mem1tb" : "memory = 1000000000000.B", - "mem2tb" : "memory = 2000000000000.B", - "mem5tb" : "memory = 5000000000000.B", - "mem10tb" : "memory = 10000000000000.B", - "mem20tb" : "memory = 20000000000000.B", - "mem50tb" : "memory = 50000000000000.B", - "mem100tb" : "memory = 100000000000000.B", - "mem200tb" : "memory = 200000000000000.B", - "mem500tb" : "memory = 500000000000000.B", - "mem1gib" : "memory = 1073741824.B", - "mem2gib" : "memory = 2147483648.B", - "mem4gib" : "memory = 4294967296.B", - "mem8gib" : "memory = 8589934592.B", - "mem16gib" : "memory = 17179869184.B", - "mem32gib" : "memory = 34359738368.B", - "mem64gib" : "memory = 68719476736.B", - "mem128gib" : "memory = 137438953472.B", - "mem256gib" : "memory = 274877906944.B", - "mem512gib" : "memory = 549755813888.B", - "mem1tib" : "memory = 1099511627776.B", - "mem2tib" : "memory = 2199023255552.B", - "mem4tib" : "memory = 4398046511104.B", - "mem8tib" : "memory = 8796093022208.B", - "mem16tib" : "memory = 17592186044416.B", - "mem32tib" : "memory = 35184372088832.B", - "mem64tib" : "memory = 70368744177664.B", - "mem128tib" : "memory = 140737488355328.B", - "mem256tib" : "memory = 281474976710656.B", - "mem512tib" : "memory = 562949953421312.B", - "cpu1" : "cpus = 1", - "cpu2" : "cpus = 2", - "cpu5" : "cpus = 5", - "cpu10" : "cpus = 10", - "cpu20" : "cpus = 20", - "cpu50" : "cpus = 50", - "cpu100" : "cpus = 100", - "cpu200" : "cpus = 200", - "cpu500" : "cpus = 500", - "cpu1000" : "cpus = 1000" - } - }, - "debug" : false, - "container" : "docker" - } - ], - "engines" : [ - { - "type" : "native", - "id" : "native" - } - ], - "build_info" : { - "config" : "/workdir/root/repo/src/workflows/rnaseq/config.vsh.yaml", - "runner" : "nextflow", - "engine" : "native", - "output" : "/workdir/root/repo/target/nextflow/workflows/rnaseq", - "viash_version" : "0.9.0", - "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", - "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" - }, - "package_config" : { - "version" : "multiple_fixes", - "info" : { - "test_resources" : [ - { - "path" : "gs://viash-hub-test-data/rnaseq/v1", - "dest" : "testData" - } - ] - }, - "repositories" : [ - { - "type" : "vsh", - "name" : "biobox", - "repo" : "vsh/biobox", - "tag" : "v0.2.0" - }, - { - "type" : "vsh", - "name" : "craftbox", - "repo" : "craftbox", - "tag" : "v0.1.0" - } - ], - "viash_version" : "0.9.0", - "source" : "/workdir/root/repo/src", - "target" : "/workdir/root/repo/target", - "config_mods" : [ - ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", - ".engines += { type: \\"native\\" }", - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'multiple_fixes'" - ], - "organization" : "vsh" - } -}''')) -] - -// resolve dependencies dependencies (if any) -meta["root_dir"] = getRootDir() -include { prepare_genome } from "${meta.resources_dir}/../../../nextflow/workflows/prepare_genome/main.nf" -include { cat_fastq } from "${meta.resources_dir}/../../../nextflow/cat_fastq/main.nf" -include { pre_processing } from "${meta.resources_dir}/../../../nextflow/workflows/pre_processing/main.nf" -include { genome_alignment_and_quant } from "${meta.resources_dir}/../../../nextflow/workflows/genome_alignment_and_quant/main.nf" -include { pseudo_alignment_and_quant } from "${meta.resources_dir}/../../../nextflow/workflows/pseudo_alignment_and_quant/main.nf" -include { post_processing } from "${meta.resources_dir}/../../../nextflow/workflows/post_processing/main.nf" -include { quality_control } from "${meta.resources_dir}/../../../nextflow/workflows/quality_control/main.nf" - -// inner workflow -// user-provided Nextflow code -workflow run_wf { - take: - input_ch - - main: - reference_ch = input_ch - - | map { id, state -> - def biotype = state.gencode ? "gene_type" : state.featurecounts_group_type - def filter_gtf = - ( - ( !state.skip_alignment && state.aligner) // Condition 1: Alignment is required and aligner is set - || ( !state.skip_pseudo_alignment && state.pseudo_aligner ) // Condition 2: Pseudoalignment is required and pseudoaligner is set - || ( !state.transcript_fasta ) // Condition 3: Transcript FASTA file is not provided - ) - && - ( !state.skip_gtf_filter ) // Condition 4: --skip_gtf_filter is not provided - [ id, state + [ biotype: biotype, filter_gtf: filter_gtf ] ] - } - - | toSortedList - - | map { list -> - [ "ref", - [ fasta: list.collect { id, state -> state.fasta }.unique()[0], - gtf: list.collect { id, state -> state.gtf }.unique()[0], - gff: list.collect { id, state -> state.gff }.unique()[0], - additional_fasta: list.collect { id, state -> state.additional_fasta }.unique()[0], - transcript_fasta:list.collect { id, state -> state.transcript_fasta }.unique()[0], - gene_bed: list.collect { id, state -> state.gene_bed }.unique()[0], - bbsplit_fasta_list: list.collect { id, state -> state.bbsplit_fasta_list }.unique()[0], - aligner: list.collect { id, state -> state.aligner }.unique()[0], - pseudo_aligner: list.collect { id, state -> state.pseudo_aligner }.unique()[0], - star_index: list.collect { id, state -> state.star_index }.unique()[0], - rsem_index: list.collect { id, state -> state.rsem_index }.unique()[0], - salmon_index: list.collect { id, state -> state.salmon_index }.unique()[0], - kallisto_index: list.collect { id, state -> state.kallisto_index }.unique()[0], - // splicesites: list.collect { id, state -> state.splicesites }.unique()[0], - // hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0], - bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0], - skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0], - gencode: list.collect { id, state -> state.gencode }.unique()[0], - biotype: list.collect { id, state -> state.biotype }.unique()[0], - filter_gtf: list.collect { id, state -> state.filter_gtf }.unique()[0], - pseudo_aligner_kmer_size: list.collect { id, state -> state.pseudo_aligner_kmer_size }.unique()[0] ] - ] - } - - // prepare all the necessary files for reference genome - | prepare_genome.run ( - fromState: [ - "fasta": "fasta", - "gtf": "gtf", - "gff": "gff", - "additional_fasta": "additional_fasta", - "transcript_fasta": "transcript_fasta", - "gene_bed": "gene_bed", - "bbsplit_fasta_list": "bbsplit_fasta_list", - "star_index": "star_index", - "rsem_index": "rsem_index", - "salmon_index": "salmon_index", - "kallisto_index": "kallisto_index", - "pseudo_aligner_kmer_size": "pseudo_aligner_kmer_size", - // "splicesites": "splicesites", - // "hisat2_index": "hisat2_index", - "bbsplit_index": "bbsplit_index", - "skip_bbsplit": "skip_bbsplit", - "gencode": "gencode", - "biotype": "biotype", - "filter_gtf": "filter_gtf", - "aligner": "aligner", - "pseudo_aligner": "pseudo_aligner" - ], - toState: [ - "fasta": "uncompressed_fasta", - "gtf": "gtf_uncompressed", - "transcript_fasta": "transcript_fasta_uncompressed", - "fai": "fai", - "chrom_sizes": "chrom_sizes", - "bbsplit_index": "bbsplit_index_uncompressed", - "star_index": "star_index_uncompressed", - "salmon_index": "salmon_index_uncompressed", - "kallisto_index": "kallisto_index_uncompressed", - "gene_bed": "gene_bed_uncompressed" - ] - ) - - // Check if contigs in genome fasta file > 512 Mbp - | map { id, state -> - (isBelowMaxContigSize(state.fai)) ? [id, state] : [id, state + [bam_csi_index: true]] - } - - | map { list -> list[1]} - - analysis_ch = input_ch - - | combine(reference_ch) - - | map { list -> [list[0], list[1] + list[2]] } - - // Concatenate FastQ files from same sample if required - | cat_fastq.run ( - fromState: [ - "read_1": "fastq_1", - "read_2": "fastq_2" - ], - toState: [ - "fastq_1": "fastq_1", - "fastq_2": "fastq_2" - ] - ) - - // Pre-process fastq files - | pre_processing.run ( - fromState: [ - "id": "id", - "fastq_1": "fastq_1", - "fastq_2": "fastq_2", - "umitools_bc_pattern": "umitools_bc_pattern", - "umitools_bc_pattern2": "umitools_bc_pattern2", - "strandedness": "strandedness", - "transcript_fasta": "transcript_fasta", - "gtf": "gtf", - "with_umi": "with_umi", - "bbsplit_index": "bbsplit_index", - "bbsplit_fasta_list": "bbsplit_fasta_list", - "bc_pattern": "bc_pattern", - "ribo_database_manifest": "ribo_database_manifest", - "salmon_index": "salmon_index", - "skip_qc": "skip_qc", - "skip_fastqc": "skip_fastqc", - "skip_skip_umi_extract": "skip_umi_extract", - "umi_discard_read": "umi_discard_read", - "skip_trimming": "skip_trimming", - "trimmer": "trimmer", - "skip_bbsplit": "skip_bbsplit", - "remove_ribo_rna": "remove_ribo_rna" - ], - toState: [ - "fastqc_html_1": "fastqc_html_1", - "fastqc_html_2": "fastqc_html_2", - "fastqc_zip_1": "fastqc_zip_1", - "fastqc_zip_2": "fastqc_zip_2", - "fastq_1": "qc_output1", - "fastq_2": "qc_output2", - "trim_log_1": "trim_log_1", - "trim_log_2": "trim_log_2", - "trim_zip_1": "trim_zip_1", - "trim_zip_2": "trim_zip_2", - "trim_html_1": "trim_html_1", - "trim_html_2": "trim_html_2", - "passed_trimmed_reads": "passed_trimmed_reads", - "num_trimmed_reads": "num_trimmed_reads", - "sortmerna_log": "sortmerna_log", - "salmon_quant_output": "salmon_quant_output", - "fastp_failed_trim": "failed_trim", - "fastp_failed_trim_unpaired1": "failed_trim_unpaired1", - "fastp_failed_trim_unpaired2": "failed_trim_unpaired2", - "fastp_trim_json": "trim_json", - "fastp_trim_html": "trim_html", - "fastp_trim_merged_out": "trim_merged_out" - ] - ) - - // Infer strandedness from Salmon pseudo-alignment results - | map { id, state -> - (state.strandedness == 'auto') ? - [ id, state + [strandedness: getSalmonInferredStrandedness(state.salmon_quant_output)] ] : - [id, state] - } - - // Filter FastQ files based on minimum trimmed read count after adapter trimming - | map { id, state -> - def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ] - def num_reads = (state.skip_trimming) ? - state.min_trimmed_reads + 1 : - ( - (state.trimmer == "fastp") ? - getFastpReadsAfterFiltering(state.fastp_trim_json) : - ( - (!state.skip_trimming && input.size() == 2) ? - getTrimGaloreReadsAfterFiltering(state.trim_log_2) : - getTrimGaloreReadsAfterFiltering(state.trim_log_1) - ) - ) - def passed_trimmed_reads = - (state.skip_trimming || (num_reads >= state.min_trimmed_reads)) ? - true : - false - [ id, state + [num_trimmed_reads: num_reads, passed_trimmed_reads: passed_trimmed_reads] ] - } - - // Genome alignment and quantification - | genome_alignment_and_quant.run ( - runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads }, - fromState: [ - "id": "id", - "fastq_1": "fastq_1", - "fastq_2": "fastq_2", - "strandedness": "strandedness", - "gtf": "gtf", - "transcript_fasta": "transcript_fasta", - "bam_csi_index": "bam_csi_index", - "aligner": "aligner", - "rsem_index": "rsem_index", - "star_index": "star_index", - "extra_star_align_args": "extra_star_align_args", - "star_ignore_sjdbgtf": "star_ignore_sjdbgtf", - "seq_platform": "seq_platform", - "seq_center": "seq_center", - "with_umi": "with_umi", - "umi_dedup_stats": "umi_dedup_stats", - "gtf_group_features": "gtf_group_features", - "gtf_extra_attributes": "gtf_extra_attributes", - "salmon_quant_libtype": "salmon_quant_libtype", - "salmon_index": "salmon_index", - "extra_rsem_calculate_expression_args": "extra_rsem_calculate_expression_args" - ], - toState: [ - "star_alignment": "star_alignment", - "star_multiqc": "star_multiqc", - "genome_bam_sorted": "genome_bam_sorted", - "genome_bam_index": "genome_bam_index", - "genome_bam_stats": "genome_bam_stats", - "genome_bam_flagstat": "genome_bam_flagstat", - "genome_bam_idxstats": "genome_bam_idxstats", - "transcriptome_bam": "transcriptome_bam", - "transcriptome_bam_index": "transcriptome_bam_index", - "transcriptome_bam_stats": "transcriptome_bam_stats", - "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", - "transcriptome_bam_idxstats": "transcriptome_bam_idxstats", - "quant_out_dir": "quant_out_dir", - "quant_results_file": "quant_results_file" - ] - ) - - // Filter channels to get samples that passed STAR minimum mapping percentage - | map { id, state -> - def percent_mapped = getStarPercentMapped(state.star_multiqc) - def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false - [ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ] - } - - // Pseudo-alignment and quantification - | pseudo_alignment_and_quant.run ( - runIf: { id, state -> !state.skip_pseudo_alignment && state.passed_trimmed_reads }, - fromState: [ - "id": "id", - "fastq_1": "fastq_1", - "fastq_2": "fastq_2", - "strandedness": "strandedness", - "gtf": "gtf", - "transcript_fasta": "transcript_fasta", - "pseudo_aligner": "pseudo_aligner", - "salmon_index": "salmon_index", - "kallisto_index": "kallisto_index", - "extra_star_align_args": "extra_star_align_args", - "star_ignore_sjdbgtf": "star_ignore_sjdbgtf", - "seq_platform": "seq_platform", - "seq_center": "seq_center", - "with_umi": "with_umi", - "umi_dedup_stats": "umi_dedup_stats", - "gtf_group_features": "gtf_group_features", - "gtf_extra_attributes": "gtf_extra_attributes", - "lib_type": "salmon_quant_libtype", - "kallisto_quant_fragment_length": "kallisto_quant_fragment_length", - "kallisto_quant_fragment_length_sd": "kallisto_quant_fragment_length_sd" - ], - toState: [ - "pseudo_quant_out_dir": "quant_out_dir", - "pseudo_salmon_quant_results_file": "salmon_quant_results_file", - "pseudo_kallisto_quant_results_file": "kallisto_quant_results_file", - "pseudo_multiqc": "pseudo_multiqc" - ] - ) - - | map { id, state -> - def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ] - def paired = input.size() == 2 - [ id, state + [ paired: paired ] ] - } - - // Post-processing - | post_processing.run ( - runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads && state.passed_mapping }, - fromState: [ - "id": "id", - "paired": "paired", - "strandedness": "strandedness", - "fasta": "fasta", - "fai": "fai", - "gtf": "gtf", - "genome_bam": "genome_bam_sorted", - "chrom_sizes": "chrom_sizes", - "star_multiqc": "star_multiqc", - "extra_picard_args": "extra_picard_args", - "extra_stringtie_args": "extra_stringtie_args", - "stringtie_ignore_gtf": "stringtie_ignore_gtf", - "extra_bedtools_args": "extra_bedtools_args", - "bam_csi_index": "bam_csi_index", - "min_mapped_reads": "min_mapped_reads", - "with_umi": "with_umi", - "skip_qc": "skip_qc", - "skip_markduplicates": "skip_markduplicates", - "skip_stringtie": "skip_stringtie", - "skip_bigwig":"gencode" - ], - toState: [ - "genome_bam_sorted": "processed_genome_bam", - "genome_bam_index": "genome_bam_index", - "genome_bam_stats": "genome_bam_stats", - "genome_bam_flagstat": "genome_bam_flagstat", - "genome_bam_idxstats": "genome_bam_idxstats", - "markduplicates_metrics": "markduplicates_metrics", - "stringtie_transcript_gtf": "stringtie_transcript_gtf", - "stringtie_coverage_gtf": "stringtie_coverage_gtf", - "stringtie_abundance": "stringtie_abundance", - "stringtie_ballgown": "stringtie_ballgown", - "bedgraph_forward": "bedgraph_forward", - "bedgraph_reverse": "bedgraph_reverse", - "bigwig_forward": "bigwig_forward", - "bigwig_reverse": "bigwig_reverse" - ] - ) - - // Final QC - | quality_control.run ( - fromState: [ - "id": "id", - "paired": "paired", - "strandedness": "strandedness", - "skip_align": "skip_alignment", - "skip_pseudo_align": "skip_pseudo_alignment", - "gtf": "gtf", - "genome_bam": "genome_bam_sorted", - "genome_bam_index": "genome_bam_index", - "quant_out_dir": "quant_out_dir", - "quant_results_file": "quant_results_file", - "pseudo_quant_out_dir": "pseudo_quant_out_dir", - "pseudo_salmon_quant_results_file": "pseudo_salmon_quant_results_file", - "pseudo_kallisto_quant_results_file": "pseudo_kallisto_quant_results_file", - "aligner": "aligner", - "pseudo_aligner": "pseudo_aligner", - "pseudo_multiqc": "pseudo_multiqc", - "gene_bed": "gene_bed", - "extra_preseq_args": "extra_preseq_args", - "extra_featurecounts_args": "extra_featurecounts_args", - "biotype": "biotype", - "biotypes_header": "biotypes_header", - "skip_biotype_qc": "skip_biotype_qc", - "featurecounts_group_type": "featurecounts_group_type", - "featurecounts_feature_type": "featurecounts_feature_type", - "gencode": "gencode", - "skip_deseq2_qc": "skip_deseq2_qc", - "extra_deseq2_args": "extra_deseq2_args", - "extra_deseq2_args2": "extra_deseq2_args2", - "multiqc_custom_config": "multiqc_custom_config", - "multiqc_title": "multiqc_title", - "multiqc_methods_description": "multiqc_methods_description", - "fastqc_zip_1": "fastqc_zip_1", - "fastqc_zip_2": "fastqc_zip_2", - "trim_log_1": "trim_log_1", - "trim_log_2": "trim_log_2", - "trim_zip_1": "trim_zip_1", - "trim_zip_2": "trim_zip_2", - "sortmerna_multiqc": "sortmerna_log", - "star_multiqc": "star_multiqc", - "genome_bam_stats": "genome_bam_stats", - "genome_bam_flagstat": "genome_bam_flagstat", - "genome_bam_idxstats": "genome_bam_idxstats", - "markduplicates_multiqc": "markduplicates_metrics", - "rseqc_modules": "rseqc_modules", - "num_trimmed_reads": "num_trimmed_reads", - "passed_trimmed_reads": "passed_trimmed_reads", - "passed_mapping": "passed_mapping", - "percent_mapped": "percent_mapped" - ], - toState: [ - "preseq_output": "preseq_output", - "bamstat_output": "bamstat_output", - "strandedness_output": "strandedness_output", - "inner_dist_output_stats": "inner_dist_output_stats", - "inner_dist_output_dist": "inner_dist_output_dist", - "inner_dist_output_freq": "inner_dist_output_freq", - "inner_dist_output_plot": "inner_dist_output_plot", - "inner_dist_output_plot_r": "inner_dist_output_plot_r", - "junction_annotation_output_log": "junction_annotation_output_log", - "junction_annotation_output_plot_r": "junction_annotation_output_plot_r", - "junction_annotation_output_junction_bed": "junction_annotation_output_junction_bed", - "junction_annotation_output_junction_interact": "junction_annotation_output_junction_interact", - "junction_annotation_output_junction_sheet": "junction_annotation_output_junction_sheet", - "junction_annotation_output_splice_events_plot": "junction_annotation_output_splice_events_plot", - "junction_annotation_output_splice_junctions_plot": "junction_annotation_output_splice_junctions_plot", - "junction_saturation_output_plot_r": "junction_saturation_output_plot_r", - "junction_saturation_output_plot": "junction_saturation_output_plot", - "read_distribution_output": "read_distribution_output", - "read_duplication_output_duplication_rate_plot_r": "read_duplication_output_duplication_rate_plot_r", - "read_duplication_output_duplication_rate_plot": "read_duplication_output_duplication_rate_plot", - "read_duplication_output_duplication_rate_mapping": "read_duplication_output_duplication_rate_mapping", - "read_duplication_output_duplication_rate_sequence": "read_duplication_output_duplication_rate_sequence", - "tin_output_summary": "tin_output_summary", - "tin_output_metrics": "tin_output_metrics", - "dupradar_output_dupmatrix": "dupradar_output_dupmatrix", - "dupradar_output_dup_intercept_mqc": "dupradar_output_dup_intercept_mqc", - "dupradar_output_duprate_exp_boxplot": "dupradar_output_duprate_exp_boxplot", - "dupradar_output_duprate_exp_densplot": "dupradar_output_duprate_exp_densplot", - "dupradar_output_duprate_exp_denscurve_mqc": "dupradar_output_duprate_exp_denscurve_mqc", - "dupradar_output_expression_histogram": "dupradar_output_expression_histogram", - "dupradar_output_intercept_slope": "dupradar_output_intercept_slope", - "qualimap_output_dir": "qualimap_output_dir", - "qualimap_output_pdf": "qualimap_output_pdf", - "featurecounts": "featurecounts", - "featurecounts_summary": "featurecounts_summary", - "featurecounts_multiqc": "featurecounts_multiqc", - "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", - "tpm_gene": "tpm_gene", - "counts_gene": "counts_gene", - "counts_gene_length_scaled": "counts_gene_length_scaled", - "counts_gene_scaled": "counts_gene_scaled", - "tpm_transcript": "tpm_transcript", - "counts_transcript": "counts_transcript", - "salmon_merged_summarizedexperiment": "salmon_merged_summarizedexperiment", - "deseq2_output": "deseq2_output", - "multiqc_report": "multiqc_report", - "multiqc_data": "multiqc_data", - "multiqc_plots": "multiqc_plots" - ] - ) - - | map { id, state -> - def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } - [ id, mod_state ] - } - - | setState ( - [ - "output_fasta": "fasta", - "output_gtf": "gtf", - "output_transcript_fasta": "transcript_fasta", - "output_gene_bed": "gene_bed", - "output_bbsplit_index": "bbsplit_index", - "output_star_index": "star_index", - "output_salmon_index": "salmon_index", - "output_kallisto_index": "kallisto_index", - "fastqc_html_1": "fastqc_html_1", - "fastqc_html_2": "fastqc_html_2", - "fastqc_zip_1": "fastqc_zip_1", - "fastqc_zip_2": "fastqc_zip_2", - "output_fastq_1": "fastq_1", - "output_fastq_2": "fastq_2", - "trim_log_1": "trim_log_1", - "trim_log_2": "trim_log_2", - "trim_zip_1": "trim_zip_1", - "trim_zip_2": "trim_zip_2", - "trim_html_1": "trim_html_1", - "trim_html_2": "trim_html_2", - "sortmerna_log": "sortmerna_log", - "star_alignment": "star_alignment", - "genome_bam_sorted": "genome_bam_sorted", - "genome_bam_index": "genome_bam_index", - "genome_bam_stats": "samtools_stats", - "genome_bam_flagstat": "samtools_flagstat", - "genome_bam_idxstats": "samtools_idxstats", - "transcriptome_bam": "transcriptome_bam", - "transcriptome_bam_index": "transcriptome_bam_index", - "transcriptome_bam_stats": "transcriptome_bam_stats", - "transcriptome_bam_flagstat": "transcriptome_bam_flagstat", - "transcriptome_bam_idxstats": "transcriptome_bam_idxstats", - "salmon_quant_results": "salmon_quant_results", - "stringtie_transcript_gtf": "stringtie_transcript_gtf", - "stringtie_coverage_gtf": "stringtie_coverage_gtf", - "stringtie_abundance": "stringtie_abundance", - "stringtie_ballgown": "stringtie_ballgown", - "featurecounts": "featurecounts", - "featurecounts_summary": "featurecounts_summary", - "featurecounts_multiqc": "featurecounts_multiqc", - "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", - "bedgraph_forward": "bedgraph_forward", - "bedgraph_reverse": "bedgraph_reverse", - "bigwig_forward": "bigwig_forward", - "bigwig_reverse": "bigwig_reverse", - "preseq_output": "preseq_output", - "bamstat_output": "bamstat_output", - "strandedness_output": "strandedness_output", - "inner_dist_output_stats": "inner_dist_output_stats", - "inner_dist_output_dist": "inner_dist_output_dist", - "inner_dist_output_freq": "inner_dist_output_freq", - "inner_dist_output_plot": "inner_dist_output_plot", - "inner_dist_output_plot_r": "inner_dist_output_plot_r", - "junction_annotation_output_log": "junction_annotation_output_log", - "junction_annotation_output_plot_r": "junction_annotation_output_plot_r", - "junction_annotation_output_junction_bed": "junction_annotation_output_junction_bed", - "junction_annotation_output_junction_interact": "junction_annotation_output_junction_interact", - "junction_annotation_output_junction_sheet": "junction_annotation_output_junction_sheet", - "junction_annotation_output_splice_events_plot": "junction_annotation_output_splice_events_plot", - "junction_annotation_output_splice_junctions_plot": "junction_annotation_output_splice_junctions_plot", - "junction_saturation_output_plot_r": "junction_saturation_output_plot_r", - "junction_saturation_output_plot": "junction_saturation_output_plot", - "read_distribution_output": "read_distribution_output", - "read_duplication_output_duplication_rate_plot_r": "read_duplication_output_duplication_rate_plot_r", - "read_duplication_output_duplication_rate_plot": "read_duplication_output_duplication_rate_plot", - "read_duplication_output_duplication_rate_mapping": "read_duplication_output_duplication_rate_mapping", - "read_duplication_output_duplication_rate_sequence": "read_duplication_output_duplication_rate_sequence", - "tin_output_summary": "tin_output_summary", - "tin_output_metrics": "tin_output_metrics", - "dupradar_output_dupmatrix": "dupradar_output_dupmatrix", - "dupradar_output_dup_intercept_mqc": "dupradar_output_dup_intercept_mqc", - "dupradar_output_duprate_exp_boxplot": "dupradar_output_duprate_exp_boxplot", - "dupradar_output_duprate_exp_densplot": "dupradar_output_duprate_exp_densplot", - "dupradar_output_duprate_exp_denscurve_mqc": "dupradar_output_duprate_exp_denscurve_mqc", - "dupradar_output_expression_histogram": "dupradar_output_expression_histogram", - "dupradar_output_intercept_slope": "dupradar_output_intercept_slope", - "qualimap_output_dir": "qualimap_output_dir", - "qualimap_output_pdf": "qualimap_output_pdf", - "tpm_gene": "tpm_gene", - "counts_gene": "counts_gene", - "counts_gene_length_scaled": "counts_gene_length_scaled", - "counts_gene_scaled": "counts_gene_scaled", - "tpm_transcript": "tpm_transcript", - "counts_transcript": "counts_transcript", - "quant_merged_summarizedexperiment": "quant_merged_summarizedexperiment", - "deseq2_output": "deseq2_output", - "pseudo_tpm_gene": "pseudo_tpm_gene", - "pseudo_counts_gene": "pseudo_counts_gene", - "pseudo_counts_gene_length_scaled": "pseudo_counts_gene_length_scaled", - "pseudo_counts_gene_scaled": "pseudo_counts_gene_scaled", - "pseudo_tpm_transcript": "pseudo_tpm_transcript", - "pseudo_counts_transcript": "pseudo_counts_transcript", - "pseudo_lengths_gene": "pseudo_lengths_gene", - "pseudo_lengths_transcript": "pseudo_lengths_transcript", - "pseudo_quant_merged_summarizedexperiment": "pseudo_quant_merged_summarizedexperiment", - "deseq2_output_pseudo": "deseq2_output_pseudo", - "multiqc_report": "multiqc_report", - "multiqc_data": "multiqc_data", - "multiqc_plots": "multiqc_plots", - "multiqc_versions": "multiqc_versions" - ] - ) - - output_ch = analysis_ch - - emit: - output_ch -} - -import nextflow.Nextflow -// -// Function to generate an error if contigs in genome fasta file > 512 Mbp -// -def isBelowMaxContigSize(fai_file) { - def max_size = 512000000 - fai_file.eachLine { line -> - def lspl = line.split('\t') - def chrom = lspl[0] - def size = lspl[1] - if (size.toInteger() > max_size) { - def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " Contig longer than ${max_size}bp found in reference genome!\n\n" + - " ${chrom}: ${size}\n\n" + - " Provide the '--bam_csi_index' parameter to use a CSI instead of BAI index.\n\n" - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - Nextflow.error(error_string) - return false - } - } - return true -} - -import groovy.json.JsonSlurper -// -// Function that parses Salmon quant 'meta_info.json' output file to get inferred strandedness -// -def getSalmonInferredStrandedness(salmon_quant_output) { - def json_file = new File(salmon_quant_output).listFiles().find { it.name == "meta_info.json" || it.isDirectory() && it.listFiles().find { it.name == "meta_info.json" } } - def lib_type = new JsonSlurper().parseText(json_file.text).get('library_types')[0] - def strandedness = 'reverse' - if (lib_type) { - if (lib_type in ['U', 'IU']) { - strandedness = 'unstranded' - } - else if (lib_type in ['SF', 'ISF']) { - strandedness = 'forward' - } - else if (lib_type in ['SR', 'ISR']) { - strandedness = 'reverse' - } - } - return strandedness -} - -// -// Function that parses TrimGalore log output file to get total number of reads after trimming -// -def getTrimGaloreReadsAfterFiltering(log_file) { - def total_reads = 0 - def filtered_reads = 0 - log_file.eachLine { line -> - def total_reads_matcher = line =~ /([\d\.]+)\ssequences processed in total/ - def filtered_reads_matcher = line =~ /shorter than the length cutoff[^:]+:\s([\d\.]+)/ - if (total_reads_matcher) total_reads = total_reads_matcher[0][1].toFloat() - if (filtered_reads_matcher) filtered_reads = filtered_reads_matcher[0][1].toFloat() - } - return total_reads - filtered_reads -} - -// -// Function that parses fastp json output file to get total number of reads after trimming -// -def getFastpReadsAfterFiltering(json_file) { - def Map json = (Map) new JsonSlurper().parseText(json_file.text).get('summary') - return json['after_filtering']['total_reads'].toLong() -} - -// -// Function that parses and returns the alignment rate from the STAR log output -// -def getStarPercentMapped(align_log) { - def percent_aligned = 0 - def pattern = /Uniquely mapped reads %\s*\|\s*([\d\.]+)%/ - align_log.eachLine { line -> - def matcher = line =~ pattern - if (matcher) { - percent_aligned = matcher[0][1].toFloat() - } - } - return percent_aligned -} - -// inner workflow hook -def innerWorkflowFactory(args) { - return run_wf -} - -// defaults -meta["defaults"] = [ - // key to be used to trace the process and determine output names - key: null, - - // fixed arguments to be passed to script - args: [:], - - // default directives - directives: readJsonBlob('''{ - "tag" : "$id" -}'''), - - // auto settings - auto: readJsonBlob('''{ - "simplifyInput" : true, - "simplifyOutput" : false, - "transcript" : false, - "publish" : false -}'''), - - // Apply a map over the incoming tuple - // Example: `{ tup -> [ tup[0], [input: tup[1].output] ] + tup.drop(2) }` - map: null, - - // Apply a map over the ID element of a tuple (i.e. the first element) - // Example: `{ id -> id + "_foo" }` - mapId: null, - - // Apply a map over the data element of a tuple (i.e. the second element) - // Example: `{ data -> [ input: data.output ] }` - mapData: null, - - // Apply a map over the passthrough elements of a tuple (i.e. the tuple excl. the first two elements) - // Example: `{ pt -> pt.drop(1) }` - mapPassthrough: null, - - // Filter the channel - // Example: `{ tup -> tup[0] == "foo" }` - filter: null, - - // Choose whether or not to run the component on the tuple if the condition is true. - // Otherwise, the tuple will be passed through. - // Example: `{ tup -> tup[0] != "skip_this" }` - runIf: null, - - // Rename keys in the data field of the tuple (i.e. the second element) - // Will likely be deprecated in favour of `fromState`. - // Example: `[ "new_key": "old_key" ]` - renameKeys: null, - - // Fetch data from the state and pass it to the module without altering the current state. - // - // `fromState` should be `null`, `List[String]`, `Map[String, String]` or a function. - // - // - If it is `null`, the state will be passed to the module as is. - // - If it is a `List[String]`, the data will be the values of the state at the given keys. - // - If it is a `Map[String, String]`, the data will be the values of the state at the given keys, with the keys renamed according to the map. - // - If it is a function, the tuple (`[id, state]`) in the channel will be passed to the function, and the result will be used as the data. - // - // Example: `{ id, state -> [input: state.fastq_file] }` - // Default: `null` - fromState: null, - - // Determine how the state should be updated after the module has been run. - // - // `toState` should be `null`, `List[String]`, `Map[String, String]` or a function. - // - // - If it is `null`, the state will be replaced with the output of the module. - // - If it is a `List[String]`, the state will be updated with the values of the data at the given keys. - // - If it is a `Map[String, String]`, the state will be updated with the values of the data at the given keys, with the keys renamed according to the map. - // - If it is a function, a tuple (`[id, output, state]`) will be passed to the function, and the result will be used as the new state. - // - // Example: `{ id, output, state -> state + [counts: state.output] }` - // Default: `{ id, output, state -> output }` - toState: null, - - // Whether or not to print debug messages - // Default: `false` - debug: false -] - -// initialise default workflow -meta["workflow"] = workflowFactory([key: meta.config.name], meta.defaults, meta) - -// add workflow to environment -nextflow.script.ScriptMeta.current().addDefinition(meta.workflow) - -// anonymous workflow for running this module as a standalone -workflow { - // add id argument if it's not already in the config - // TODO: deep copy - def newConfig = deepClone(meta.config) - def newParams = deepClone(params) - - def argsContainsId = newConfig.allArguments.any{it.plainName == "id"} - if (!argsContainsId) { - def idArg = [ - 'name': '--id', - 'required': false, - 'type': 'string', - 'description': 'A unique id for every entry.', - 'multiple': false - ] - newConfig.arguments.add(0, idArg) - newConfig = processConfig(newConfig) - } - if (!newParams.containsKey("id")) { - newParams.id = "run" - } - - helpMessage(newConfig) - - channelFromParams(newParams, newConfig) - // make sure id is not in the state if id is not in the args - | map {id, state -> - if (!argsContainsId) { - [id, state.findAll{k, v -> k != "id"}] - } else { - [id, state] - } - } - | meta.workflow.run( - auto: [ publish: "state" ] - ) -} - -// END COMPONENT-SPECIFIC CODE diff --git a/target/nextflow/workflows/rnaseq/nextflow.config b/target/nextflow/workflows/rnaseq/nextflow.config deleted file mode 100644 index 6024181..0000000 --- a/target/nextflow/workflows/rnaseq/nextflow.config +++ /dev/null @@ -1,125 +0,0 @@ -manifest { - name = 'workflows/rnaseq' - mainScript = 'main.nf' - nextflowVersion = '!>=20.12.1-edge' - version = 'multiple_fixes' - description = 'A viash workflow for the nf-core/rnaseq pipeline.\n' -} - -process.container = 'nextflow/bash:latest' - -// detect tempdir -tempDir = java.nio.file.Paths.get( - System.getenv('NXF_TEMP') ?: - System.getenv('VIASH_TEMP') ?: - System.getenv('TEMPDIR') ?: - System.getenv('TMPDIR') ?: - '/tmp' -).toAbsolutePath() - -profiles { - no_publish { - process { - withName: '.*' { - publishDir = [ - enabled: false - ] - } - } - } - mount_temp { - docker.temp = tempDir - podman.temp = tempDir - charliecloud.temp = tempDir - } - docker { - docker.enabled = true - // docker.userEmulation = true - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - } - singularity { - singularity.enabled = true - singularity.autoMounts = true - docker.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - } - podman { - podman.enabled = true - docker.enabled = false - singularity.enabled = false - shifter.enabled = false - charliecloud.enabled = false - } - shifter { - shifter.enabled = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - charliecloud.enabled = false - } - charliecloud { - charliecloud.enabled = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - } -} - -process{ - withLabel: mem1gb { memory = 1000000000.B } - withLabel: mem2gb { memory = 2000000000.B } - withLabel: mem5gb { memory = 5000000000.B } - withLabel: mem10gb { memory = 10000000000.B } - withLabel: mem20gb { memory = 20000000000.B } - withLabel: mem50gb { memory = 50000000000.B } - withLabel: mem100gb { memory = 100000000000.B } - withLabel: mem200gb { memory = 200000000000.B } - withLabel: mem500gb { memory = 500000000000.B } - withLabel: mem1tb { memory = 1000000000000.B } - withLabel: mem2tb { memory = 2000000000000.B } - withLabel: mem5tb { memory = 5000000000000.B } - withLabel: mem10tb { memory = 10000000000000.B } - withLabel: mem20tb { memory = 20000000000000.B } - withLabel: mem50tb { memory = 50000000000000.B } - withLabel: mem100tb { memory = 100000000000000.B } - withLabel: mem200tb { memory = 200000000000000.B } - withLabel: mem500tb { memory = 500000000000000.B } - withLabel: mem1gib { memory = 1073741824.B } - withLabel: mem2gib { memory = 2147483648.B } - withLabel: mem4gib { memory = 4294967296.B } - withLabel: mem8gib { memory = 8589934592.B } - withLabel: mem16gib { memory = 17179869184.B } - withLabel: mem32gib { memory = 34359738368.B } - withLabel: mem64gib { memory = 68719476736.B } - withLabel: mem128gib { memory = 137438953472.B } - withLabel: mem256gib { memory = 274877906944.B } - withLabel: mem512gib { memory = 549755813888.B } - withLabel: mem1tib { memory = 1099511627776.B } - withLabel: mem2tib { memory = 2199023255552.B } - withLabel: mem4tib { memory = 4398046511104.B } - withLabel: mem8tib { memory = 8796093022208.B } - withLabel: mem16tib { memory = 17592186044416.B } - withLabel: mem32tib { memory = 35184372088832.B } - withLabel: mem64tib { memory = 70368744177664.B } - withLabel: mem128tib { memory = 140737488355328.B } - withLabel: mem256tib { memory = 281474976710656.B } - withLabel: mem512tib { memory = 562949953421312.B } - withLabel: cpu1 { cpus = 1 } - withLabel: cpu2 { cpus = 2 } - withLabel: cpu5 { cpus = 5 } - withLabel: cpu10 { cpus = 10 } - withLabel: cpu20 { cpus = 20 } - withLabel: cpu50 { cpus = 50 } - withLabel: cpu100 { cpus = 100 } - withLabel: cpu200 { cpus = 200 } - withLabel: cpu500 { cpus = 500 } - withLabel: cpu1000 { cpus = 1000 } -} - - diff --git a/target/nextflow/workflows/rnaseq/nextflow_schema.json b/target/nextflow/workflows/rnaseq/nextflow_schema.json deleted file mode 100644 index 0638401..0000000 --- a/target/nextflow/workflows/rnaseq/nextflow_schema.json +++ /dev/null @@ -1,2070 +0,0 @@ -{ -"$schema": "http://json-schema.org/draft-07/schema", -"title": "rnaseq", -"description": "A viash workflow for the nf-core/rnaseq pipeline.\n", -"type": "object", -"definitions": { - - - - "input" : { - "title": "Input", - "type": "object", - "description": "No description", - "properties": { - - - "id": { - "type": - "string", - "description": "Type: `string`, required, example: `foo`. ID of the sample", - "help_text": "Type: `string`, required, example: `foo`. ID of the sample." - - } - - - , - "fastq_1": { - "type": - "string", - "description": "Type: List of `file`, required, multiple_sep: `\";\"`. Path to the sample (or read 1 of paired end sample)", - "help_text": "Type: List of `file`, required, multiple_sep: `\";\"`. Path to the sample (or read 1 of paired end sample)." - - } - - - , - "fastq_2": { - "type": - "string", - "description": "Type: List of `file`, multiple_sep: `\";\"`. Path to read 2 of the sample", - "help_text": "Type: List of `file`, multiple_sep: `\";\"`. Path to read 2 of the sample." - - } - - - , - "strandedness": { - "type": - "string", - "description": "Type: `string`, default: `auto`, choices: ``unstranded`, `forward`, `reverse`, `auto``. Sample strand-specificity", - "help_text": "Type: `string`, default: `auto`, choices: ``unstranded`, `forward`, `reverse`, `auto``. Sample strand-specificity. Must be one of unstranded, forward, reverse or auto", - "enum": ["unstranded", "forward", "reverse", "auto"] - - , - "default": "auto" - } - - -} -}, - - - "reference genome options" : { - "title": "Reference genome options", - "type": "object", - "description": "No description", - "properties": { - - - "fasta": { - "type": - "string", - "description": "Type: `file`, required. Path to FASTA genome file", - "help_text": "Type: `file`, required. Path to FASTA genome file." - - } - - - , - "gtf": { - "type": - "string", - "description": "Type: `file`. Path to GTF annotation file", - "help_text": "Type: `file`. Path to GTF annotation file. This parameter is *mandatory* if --genome is not specified." - - } - - - , - "gff": { - "type": - "string", - "description": "Type: `file`. Path to GFF3 annotation file", - "help_text": "Type: `file`. Path to GFF3 annotation file. Required if \"--gtf\" is not specified." - - } - - - , - "additional_fasta": { - "type": - "string", - "description": "Type: `file`. FASTA file to concatenate to genome FASTA file e", - "help_text": "Type: `file`. FASTA file to concatenate to genome FASTA file e.g. containing spike-in sequences." - - } - - - , - "transcript_fasta": { - "type": - "string", - "description": "Type: `file`. Path to FASTA transcriptome file", - "help_text": "Type: `file`. Path to FASTA transcriptome file." - - } - - - , - "gene_bed": { - "type": - "string", - "description": "Type: `file`. Path to BED file containing gene intervals", - "help_text": "Type: `file`. Path to BED file containing gene intervals. This will be created from the GTF file if not specified." - - } - - - , - "splicesites": { - "type": - "string", - "description": "Type: `file`. Splice sites file required for HISAT2", - "help_text": "Type: `file`. Splice sites file required for HISAT2." - - } - - - , - "star_index": { - "type": - "string", - "description": "Type: `file`. Path to directory or tar", - "help_text": "Type: `file`. Path to directory or tar.gz archive for pre-built STAR index." - - } - - - , - "rsem_index": { - "type": - "string", - "description": "Type: `file`. Path to directory or tar", - "help_text": "Type: `file`. Path to directory or tar.gz archive for pre-built RSEM index." - - } - - - , - "salmon_index": { - "type": - "string", - "description": "Type: `file`. Path to directory or tar", - "help_text": "Type: `file`. Path to directory or tar.gz archive for pre-built Salmon index." - - } - - - , - "kallisto_index": { - "type": - "string", - "description": "Type: `file`. Path to directory or tar", - "help_text": "Type: `file`. Path to directory or tar.gz archive for pre-built Kallisto index." - - } - - - , - "gencode": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Specify if the GTF annotation is in GENCODE format", - "help_text": "Type: `boolean_true`, default: `false`. Specify if the GTF annotation is in GENCODE format." - , - "default": "False" - } - - - , - "gtf_extra_attributes": { - "type": - "string", - "description": "Type: `string`, default: `gene_name`. Additional gene identifiers from the input GTF file when running Salmon", - "help_text": "Type: `string`, default: `gene_name`. Additional gene identifiers from the input GTF file when running Salmon. More than one value can be specified separated by comma." - , - "default": "gene_name" - } - - - , - "gtf_group_features": { - "type": - "string", - "description": "Type: `string`, default: `gene_id`. Define the attribute type used to group features in the GTF file when running Salmon", - "help_text": "Type: `string`, default: `gene_id`. Define the attribute type used to group features in the GTF file when running Salmon." - , - "default": "gene_id" - } - - - , - "featurecounts_group_type": { - "type": - "string", - "description": "Type: `string`, default: `gene_biotype`. The attribute type used to group feature types in the GTF file when generating the biotype plot with featureCounts", - "help_text": "Type: `string`, default: `gene_biotype`. The attribute type used to group feature types in the GTF file when generating the biotype plot with featureCounts." - , - "default": "gene_biotype" - } - - - , - "featurecounts_feature_type": { - "type": - "string", - "description": "Type: `string`, default: `exon`. By default, the pipeline assigns reads based on the \u0027exon\u0027 attribute within the GTF file", - "help_text": "Type: `string`, default: `exon`. By default, the pipeline assigns reads based on the \u0027exon\u0027 attribute within the GTF file." - , - "default": "exon" - } - - -} -}, - - - "read trimming options" : { - "title": "Read trimming options", - "type": "object", - "description": "No description", - "properties": { - - - "trimmer": { - "type": - "string", - "description": "Type: `string`, default: `trimgalore`, choices: ``trimgalore`, `fastp``. Specify the trimming tool to use", - "help_text": "Type: `string`, default: `trimgalore`, choices: ``trimgalore`, `fastp``. Specify the trimming tool to use.", - "enum": ["trimgalore", "fastp"] - - , - "default": "trimgalore" - } - - - , - "extra_trimgalore_args": { - "type": - "string", - "description": "Type: `string`. Extra arguments to pass to Trim Galore! command in addition to defaults defined by the pipeline", - "help_text": "Type: `string`. Extra arguments to pass to Trim Galore! command in addition to defaults defined by the pipeline." - - } - - - , - "extra_fastp_args": { - "type": - "string", - "description": "Type: `string`. Extra arguments to pass to fastp command in addition to defaults defined by the pipeline", - "help_text": "Type: `string`. Extra arguments to pass to fastp command in addition to defaults defined by the pipeline." - - } - - - , - "min_trimmed_reads": { - "type": - "integer", - "description": "Type: `integer`, default: `10000`. Minimum number of trimmed reads below which samples are removed from further processing", - "help_text": "Type: `integer`, default: `10000`. Minimum number of trimmed reads below which samples are removed from further processing. Some downstream steps in the pipeline will fail if this threshold is too low." - , - "default": "10000" - } - - -} -}, - - - "read filtering options" : { - "title": "Read filtering options", - "type": "object", - "description": "No description", - "properties": { - - - "bbsplit_fasta_list": { - "type": - "string", - "description": "Type: `file`. Path to comma-separated file containing a list of reference genomes to filter reads against with BBSplit", - "help_text": "Type: `file`. Path to comma-separated file containing a list of reference genomes to filter reads against with BBSplit. To use BBSplit, \"--skip_bbsplit\" must be explicitly set to \"false\". The file should contain 2 (comma separated) columns - short name and full path to reference genome(s)" - - } - - - , - "bbsplit_index": { - "type": - "string", - "description": "Type: `file`. Path to directory or tar", - "help_text": "Type: `file`. Path to directory or tar.gz archive for pre-built BBSplit index." - - } - - - , - "remove_ribo_rna": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Enable the removal of reads derived from ribosomal RNA using SortMeRNA", - "help_text": "Type: `boolean_true`, default: `false`. Enable the removal of reads derived from ribosomal RNA using SortMeRNA." - , - "default": "False" - } - - - , - "ribo_database_manifest": { - "type": - "string", - "description": "Type: `file`, default: `assets/rrna-db-defaults.txt`. Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA", - "help_text": "Type: `file`, default: `assets/rrna-db-defaults.txt`. Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA." - , - "default": "assets/rrna-db-defaults.txt" - } - - -} -}, - - - "umi options" : { - "title": "UMI options", - "type": "object", - "description": "No description", - "properties": { - - - "with_umi": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Enable UMI-based read deduplication", - "help_text": "Type: `boolean_true`, default: `false`. Enable UMI-based read deduplication." - , - "default": "False" - } - - - , - "umitools_extract_method": { - "type": - "string", - "description": "Type: `string`, default: `string`, choices: ``string`, `regex``. UMI pattern to use", - "help_text": "Type: `string`, default: `string`, choices: ``string`, `regex``. UMI pattern to use.", - "enum": ["string", "regex"] - - , - "default": "string" - } - - - , - "umitools_bc_pattern": { - "type": - "string", - "description": "Type: `string`. The UMI barcode pattern to use e", - "help_text": "Type: `string`. The UMI barcode pattern to use e.g. \u0027NNNNNN\u0027 indicates that the first 6 nucleotides of the read are from the UMI." - - } - - - , - "umitools_bc_pattern2": { - "type": - "string", - "description": "Type: `string`. The UMI barcode pattern to use if the UMI is located in read 2", - "help_text": "Type: `string`. The UMI barcode pattern to use if the UMI is located in read 2." - - } - - - , - "umi_discard_read": { - "type": - "integer", - "description": "Type: `integer`, default: `0`, choices: ``0`, `1`, `2``. After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively", - "help_text": "Type: `integer`, default: `0`, choices: ``0`, `1`, `2``. After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively.", - "enum": [0, 1, 2] - - , - "default": "0" - } - - - , - "umitools_umi_separator": { - "type": - "string", - "description": "Type: `string`, default: `_`. The character that separates the UMI in the read name", - "help_text": "Type: `string`, default: `_`. The character that separates the UMI in the read name. Most likely a colon if you skipped the extraction with UMI-tools and used other software." - , - "default": "_" - } - - - , - "umitools_grouping_method": { - "type": - "string", - "description": "Type: `string`, default: `directional`, choices: ``unique`, `percentile`, `cluster`, `adjacency`, `directional``. Method to use to determine read groups by subsuming those with similar UMIs", - "help_text": "Type: `string`, default: `directional`, choices: ``unique`, `percentile`, `cluster`, `adjacency`, `directional``. Method to use to determine read groups by subsuming those with similar UMIs. All methods start by identifying the reads with the same mapping position, but treat similar yet nonidentical UMIs differently.", - "enum": ["unique", "percentile", "cluster", "adjacency", "directional"] - - , - "default": "directional" - } - - - , - "umi_dedup_stats": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Generate output stats when running \"umi_tools dedup\"", - "help_text": "Type: `boolean_true`, default: `false`. Generate output stats when running \"umi_tools dedup\"." - , - "default": "False" - } - - -} -}, - - - "alignment options" : { - "title": "Alignment options", - "type": "object", - "description": "No description", - "properties": { - - - "aligner": { - "type": - "string", - "description": "Type: `string`, default: `star_salmon`, choices: ``star_salmon`, `star_rsem`, `hisat2``. Specifies the alignment algorithm to use - available options are \u0027star_salmon\u0027, \u0027star_rsem\u0027 and \u0027hisat2\u0027", - "help_text": "Type: `string`, default: `star_salmon`, choices: ``star_salmon`, `star_rsem`, `hisat2``. Specifies the alignment algorithm to use - available options are \u0027star_salmon\u0027, \u0027star_rsem\u0027 and \u0027hisat2\u0027.", - "enum": ["star_salmon", "star_rsem", "hisat2"] - - , - "default": "star_salmon" - } - - - , - "pseudo_aligner": { - "type": - "string", - "description": "Type: `string`, default: `salmon`, choices: ``salmon`, `kallisto``. Specifies the pseudo aligner to use - available options are \u0027salmon\u0027", - "help_text": "Type: `string`, default: `salmon`, choices: ``salmon`, `kallisto``. Specifies the pseudo aligner to use - available options are \u0027salmon\u0027. Runs in addition to \u0027--aligner\u0027.", - "enum": ["salmon", "kallisto"] - - , - "default": "salmon" - } - - - , - "pseudo_aligner_kmer_size": { - "type": - "integer", - "description": "Type: `integer`, default: `31`. Kmer length passed to indexing step of pseudoaligners", - "help_text": "Type: `integer`, default: `31`. Kmer length passed to indexing step of pseudoaligners." - , - "default": "31" - } - - - , - "kallisto_quant_fragment_length": { - "type": - "integer", - "description": "Type: `integer`. For single-end mode only, the estimated average fragment length to use for quantification with Kallisto", - "help_text": "Type: `integer`. For single-end mode only, the estimated average fragment length to use for quantification with Kallisto." - - } - - - , - "kallisto_quant_fragment_length_sd": { - "type": - "integer", - "description": "Type: `integer`. For single-end mode only, the estimated standard deviation of the fragment length for quantification with Kallisto", - "help_text": "Type: `integer`. For single-end mode only, the estimated standard deviation of the fragment length for quantification with Kallisto." - - } - - - , - "bam_csi_index": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Create a CSI index for BAM files instead of the traditional BAI index", - "help_text": "Type: `boolean_true`, default: `false`. Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes." - , - "default": "False" - } - - - , - "salmon_quant_libtype": { - "type": - "string", - "description": "Type: `string`. Override Salmon library type inferred based on strandedness defined in meta object", - "help_text": "Type: `string`. Override Salmon library type inferred based on strandedness defined in meta object." - - } - - - , - "extra_salmon_quant_args": { - "type": - "string", - "description": "Type: `string`, default: `-v`. Extra arguments to pass to salmon quant command in addition to defaults defined by the pipeline", - "help_text": "Type: `string`, default: `-v`. Extra arguments to pass to salmon quant command in addition to defaults defined by the pipeline." - , - "default": "-v" - } - - - , - "min_mapped_reads": { - "type": - "integer", - "description": "Type: `integer`, default: `5`. Minimum percentage of uniquely mapped reads below which samples are removed from further processing", - "help_text": "Type: `integer`, default: `5`. Minimum percentage of uniquely mapped reads below which samples are removed from further processing." - , - "default": "5" - } - - - , - "stringtie_ignore_gtf": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Perform reference-guided de novo assembly of transcripts using StringTie, i", - "help_text": "Type: `boolean_true`, default: `false`. Perform reference-guided de novo assembly of transcripts using StringTie, i.e. don\u0027t restrict to those in GTF file." - , - "default": "False" - } - - - , - "extra_stringtie_args": { - "type": - "string", - "description": "Type: `string`, default: `-v`. Extra arguments to pass to stringtie command in addition to defaults defined by the pipeline", - "help_text": "Type: `string`, default: `-v`. Extra arguments to pass to stringtie command in addition to defaults defined by the pipeline." - , - "default": "-v" - } - - - , - "save_unaligned": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Where possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory", - "help_text": "Type: `boolean_true`, default: `false`. Where possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory." - , - "default": "False" - } - - - , - "save_align_intermeds": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Save the intermediate BAM files from the alignment step", - "help_text": "Type: `boolean_true`, default: `false`. Save the intermediate BAM files from the alignment step." - , - "default": "False" - } - - - , - "skip_alignment": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Skip all of the alignment-based processes within the pipeline", - "help_text": "Type: `boolean_true`, default: `false`. Skip all of the alignment-based processes within the pipeline." - , - "default": "False" - } - - - , - "skip_pseudo_alignment": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Skip all of the pseudo-alignment-based processes within the pipeline", - "help_text": "Type: `boolean_true`, default: `false`. Skip all of the pseudo-alignment-based processes within the pipeline." - , - "default": "False" - } - - - , - "extra_rsem_calculate_expression_args": { - "type": - "string", - "description": "Type: `string`, default: `--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1`. Extra arguments to pass to rsem-calculate-expression command in addition to defaults defined by the pipeline", - "help_text": "Type: `string`, default: `--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1`. Extra arguments to pass to rsem-calculate-expression command in addition to defaults defined by the pipeline." - , - "default": "--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1" - } - - -} -}, - - - "process skipping options" : { - "title": "Process skipping options", - "type": "object", - "description": "No description", - "properties": { - - - "skip_fastqc": { - "type": - "boolean", - "description": "Type: `boolean`, default: `false`. Skip FatQC step", - "help_text": "Type: `boolean`, default: `false`. Skip FatQC step." - , - "default": "False" - } - - - , - "skip_trimming": { - "type": - "boolean", - "description": "Type: `boolean`, default: `false`. Skip the adapter trimming step", - "help_text": "Type: `boolean`, default: `false`. Skip the adapter trimming step." - , - "default": "False" - } - - - , - "skip_bbsplit": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Skip BBSplit for removal of non-reference genome reads", - "help_text": "Type: `boolean_true`, default: `false`. Skip BBSplit for removal of non-reference genome reads." - , - "default": "False" - } - - - , - "skip_umi_extract": { - "type": - "boolean", - "description": "Type: `boolean`, default: `false`. Skip umi_tools extract step", - "help_text": "Type: `boolean`, default: `false`. Skip umi_tools extract step." - , - "default": "False" - } - - - , - "skip_qc": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Skip all QC steps except for MultiQC", - "help_text": "Type: `boolean_true`, default: `false`. Skip all QC steps except for MultiQC." - , - "default": "False" - } - - - , - "skip_markduplicates": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Skip picard MarkDuplicates step", - "help_text": "Type: `boolean_true`, default: `false`. Skip picard MarkDuplicates step." - , - "default": "False" - } - - - , - "skip_stringtie": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Skip StringTie", - "help_text": "Type: `boolean_true`, default: `false`. Skip StringTie." - , - "default": "False" - } - - - , - "skip_biotype_qc": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Skip additional featureCounts process for biotype QC", - "help_text": "Type: `boolean_true`, default: `false`. Skip additional featureCounts process for biotype QC." - , - "default": "False" - } - - - , - "skip_bigwig": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Skip bigWig file creation", - "help_text": "Type: `boolean_true`, default: `false`. Skip bigWig file creation." - , - "default": "False" - } - - - , - "skip_preseq": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Skip Preseq", - "help_text": "Type: `boolean_true`, default: `false`. Skip Preseq." - , - "default": "False" - } - - - , - "skip_deseq2_qc": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Skip DESeq2 PCA and heatmap plotting", - "help_text": "Type: `boolean_true`, default: `false`. Skip DESeq2 PCA and heatmap plotting." - , - "default": "False" - } - - - , - "skip_dupradar": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Skip dupRadar", - "help_text": "Type: `boolean_true`, default: `false`. Skip dupRadar." - , - "default": "False" - } - - - , - "skip_rseqc": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Skip RSeQC", - "help_text": "Type: `boolean_true`, default: `false`. Skip RSeQC." - , - "default": "False" - } - - - , - "skip_multiqc": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Skip MultiQC", - "help_text": "Type: `boolean_true`, default: `false`. Skip MultiQC." - , - "default": "False" - } - - -} -}, - - - "other process arguments" : { - "title": "Other process arguments", - "type": "object", - "description": "No description", - "properties": { - - - "extra_fq_subsample_args": { - "type": - "string", - "description": "Type: `string`, default: ` --record-count 1000000 --seed 1`. Extra arguments to pass to fq subsample command in addition to defaults defined by the pipeline", - "help_text": "Type: `string`, default: ` --record-count 1000000 --seed 1`. Extra arguments to pass to fq subsample command in addition to defaults defined by the pipeline." - , - "default": " --record-count 1000000 --seed 1" - } - - - , - "extra_picard_args": { - "type": - "string", - "description": "Type: `string`, default: ` --ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp`. Extra arguments to pass to picard MarkDuplicates command in addition to defaults defined by the pipeline", - "help_text": "Type: `string`, default: ` --ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp`. Extra arguments to pass to picard MarkDuplicates command in addition to defaults defined by the pipeline." - , - "default": " --ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp" - } - - - , - "extra_bedtools_args": { - "type": - "string", - "description": "Type: `string`, default: ` -split -du`. Extra arguments to pass to bedtools genomecov command in addition to defaults defined by the pipeline", - "help_text": "Type: `string`, default: ` -split -du`. Extra arguments to pass to bedtools genomecov command in addition to defaults defined by the pipeline." - , - "default": " -split -du" - } - - - , - "extra_featurecounts_args": { - "type": - "string", - "description": "Type: `string`, default: ` -B -C`. Extra arguments to pass to featureCounts command in addition to defaults defined by the pipeline", - "help_text": "Type: `string`, default: ` -B -C`. Extra arguments to pass to featureCounts command in addition to defaults defined by the pipeline" - , - "default": " -B -C" - } - - - , - "extra_preseq_args": { - "type": - "string", - "description": "Type: `string`, default: `-verbose -seed 1 -seg_len 100000000`. Extra arguments to pass to preseq lc_extrap command in addition to defaults defined by the pipeline", - "help_text": "Type: `string`, default: `-verbose -seed 1 -seg_len 100000000`. Extra arguments to pass to preseq lc_extrap command in addition to defaults defined by the pipeline" - , - "default": "-verbose -seed 1 -seg_len 100000000" - } - - - , - "pca_header_multiqc": { - "type": - "string", - "description": "Type: `file`, default: `assets/multiqc/deseq2_pca_header.txt`. ", - "help_text": "Type: `file`, default: `assets/multiqc/deseq2_pca_header.txt`. " - , - "default": "assets/multiqc/deseq2_pca_header.txt" - } - - - , - "clustering_header_multiqc": { - "type": - "string", - "description": "Type: `file`, default: `assets/multiqc/deseq2_clustering_header.txt`. ", - "help_text": "Type: `file`, default: `assets/multiqc/deseq2_clustering_header.txt`. " - , - "default": "assets/multiqc/deseq2_clustering_header.txt" - } - - - , - "deseq2_vst": { - "type": - "boolean", - "description": "Type: `boolean`, default: `true`. Use vst transformation instead of rlog with DESeq2", - "help_text": "Type: `boolean`, default: `true`. Use vst transformation instead of rlog with DESeq2" - , - "default": "True" - } - - - , - "extra_deseq2_args": { - "type": - "string", - "description": "Type: `string`, default: `--id_col 1 --sample_suffix \u0027\u0027 --outprefix deseq2 --count_col 3`. ", - "help_text": "Type: `string`, default: `--id_col 1 --sample_suffix \u0027\u0027 --outprefix deseq2 --count_col 3`. " - , - "default": "--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3" - } - - - , - "extra_deseq2_args2": { - "type": - "string", - "description": "Type: `string`, default: `star_salmon`. ", - "help_text": "Type: `string`, default: `star_salmon`. " - , - "default": "star_salmon" - } - - - , - "rseqc_modules": { - "type": - "string", - "description": "Type: List of `string`, default: `bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication`, multiple_sep: `\",\"`, choices: ``bam_stat`, `inner_distance`, `infer_experiment`, `junction_annotation`, `junction_saturation`, `read_distribution`, `read_duplication`, `tin``. Specify the RSeQC modules to run_wf", - "help_text": "Type: List of `string`, default: `bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication`, multiple_sep: `\",\"`, choices: ``bam_stat`, `inner_distance`, `infer_experiment`, `junction_annotation`, `junction_saturation`, `read_distribution`, `read_duplication`, `tin``. Specify the RSeQC modules to run_wf", - "enum": ["bam_stat", "inner_distance", "infer_experiment", "junction_annotation", "junction_saturation", "read_distribution", "read_duplication", "tin"] - - , - "default": "bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication" - } - - -} -}, - - - "multiqc paramenters" : { - "title": "Multiqc paramenters", - "type": "object", - "description": "No description", - "properties": { - - - "multiqc_custom_config": { - "type": - "string", - "description": "Type: `file`, default: `assets/multiqc_config.yml`. ", - "help_text": "Type: `file`, default: `assets/multiqc_config.yml`. " - , - "default": "assets/multiqc_config.yml" - } - - - , - "multiqc_title": { - "type": - "string", - "description": "Type: `string`. ", - "help_text": "Type: `string`. " - - } - - - , - "multiqc_methods_description": { - "type": - "string", - "description": "Type: `file`, default: `assets/methods_description_template.yml`. ", - "help_text": "Type: `file`, default: `assets/methods_description_template.yml`. " - , - "default": "assets/methods_description_template.yml" - } - - -} -}, - - - "output" : { - "title": "Output", - "type": "object", - "description": "No description", - "properties": { - - - "output_fasta": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_fasta.fasta`. ", - "help_text": "Type: `file`, default: `$id.$key.output_fasta.fasta`. " - , - "default": "$id.$key.output_fasta.fasta" - } - - - , - "output_gtf": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_gtf.gtf`. ", - "help_text": "Type: `file`, default: `$id.$key.output_gtf.gtf`. " - , - "default": "$id.$key.output_gtf.gtf" - } - - - , - "output_transcript_fasta": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_transcript_fasta.fasta`. ", - "help_text": "Type: `file`, default: `$id.$key.output_transcript_fasta.fasta`. " - , - "default": "$id.$key.output_transcript_fasta.fasta" - } - - - , - "output_gene_bed": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_gene_bed.bed`. ", - "help_text": "Type: `file`, default: `$id.$key.output_gene_bed.bed`. " - , - "default": "$id.$key.output_gene_bed.bed" - } - - - , - "output_star_index": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_star_index.output_star_index`. Path to STAR index", - "help_text": "Type: `file`, default: `$id.$key.output_star_index.output_star_index`. Path to STAR index." - , - "default": "$id.$key.output_star_index.output_star_index" - } - - - , - "output_salmon_index": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_salmon_index.output_salmon_index`. Path to Salmon index", - "help_text": "Type: `file`, default: `$id.$key.output_salmon_index.output_salmon_index`. Path to Salmon index." - , - "default": "$id.$key.output_salmon_index.output_salmon_index" - } - - - , - "output_bbsplit_index": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_bbsplit_index.output_bbsplit_index`. Path to BBSplit index", - "help_text": "Type: `file`, default: `$id.$key.output_bbsplit_index.output_bbsplit_index`. Path to BBSplit index." - , - "default": "$id.$key.output_bbsplit_index.output_bbsplit_index" - } - - - , - "output_kallisto_index": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_kallisto_index.output_kallisto_index`. Path to Kallisto index", - "help_text": "Type: `file`, default: `$id.$key.output_kallisto_index.output_kallisto_index`. Path to Kallisto index." - , - "default": "$id.$key.output_kallisto_index.output_kallisto_index" - } - - - , - "output_fastq_1": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_fastq_1.fastq`. Path to output directory", - "help_text": "Type: `file`, default: `$id.$key.output_fastq_1.fastq`. Path to output directory" - , - "default": "$id.$key.output_fastq_1.fastq" - } - - - , - "output_fastq_2": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_fastq_2.fastq`. Path to output directory", - "help_text": "Type: `file`, default: `$id.$key.output_fastq_2.fastq`. Path to output directory" - , - "default": "$id.$key.output_fastq_2.fastq" - } - - - , - "fastqc_html_1": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.fastqc_html_1.html`. FastQC HTML report for read 1", - "help_text": "Type: `file`, default: `$id.$key.fastqc_html_1.html`. FastQC HTML report for read 1." - , - "default": "$id.$key.fastqc_html_1.html" - } - - - , - "fastqc_html_2": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.fastqc_html_2.html`. FastQC HTML report for read 2", - "help_text": "Type: `file`, default: `$id.$key.fastqc_html_2.html`. FastQC HTML report for read 2." - , - "default": "$id.$key.fastqc_html_2.html" - } - - - , - "fastqc_zip_1": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.fastqc_zip_1.zip`. FastQC report archive for read 1", - "help_text": "Type: `file`, default: `$id.$key.fastqc_zip_1.zip`. FastQC report archive for read 1." - , - "default": "$id.$key.fastqc_zip_1.zip" - } - - - , - "fastqc_zip_2": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.fastqc_zip_2.zip`. FastQC report archive for read 2", - "help_text": "Type: `file`, default: `$id.$key.fastqc_zip_2.zip`. FastQC report archive for read 2." - , - "default": "$id.$key.fastqc_zip_2.zip" - } - - - , - "trim_log_1": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.trim_log_1.txt`. ", - "help_text": "Type: `file`, default: `$id.$key.trim_log_1.txt`. " - , - "default": "$id.$key.trim_log_1.txt" - } - - - , - "trim_log_2": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.trim_log_2.txt`. ", - "help_text": "Type: `file`, default: `$id.$key.trim_log_2.txt`. " - , - "default": "$id.$key.trim_log_2.txt" - } - - - , - "trim_html_1": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.trim_html_1.html`. ", - "help_text": "Type: `file`, default: `$id.$key.trim_html_1.html`. " - , - "default": "$id.$key.trim_html_1.html" - } - - - , - "trim_html_2": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.trim_html_2.html`. ", - "help_text": "Type: `file`, default: `$id.$key.trim_html_2.html`. " - , - "default": "$id.$key.trim_html_2.html" - } - - - , - "trim_zip_1": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.trim_zip_1.zip`. ", - "help_text": "Type: `file`, default: `$id.$key.trim_zip_1.zip`. " - , - "default": "$id.$key.trim_zip_1.zip" - } - - - , - "trim_zip_2": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.trim_zip_2.zip`. ", - "help_text": "Type: `file`, default: `$id.$key.trim_zip_2.zip`. " - , - "default": "$id.$key.trim_zip_2.zip" - } - - - , - "sortmerna_log": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.sortmerna_log.log`. Sortmerna log file", - "help_text": "Type: `file`, default: `$id.$key.sortmerna_log.log`. Sortmerna log file." - , - "default": "$id.$key.sortmerna_log.log" - } - - - , - "star_alignment": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.star_alignment.star_alignment`. ", - "help_text": "Type: `file`, default: `$id.$key.star_alignment.star_alignment`. " - , - "default": "$id.$key.star_alignment.star_alignment" - } - - - , - "genome_bam_sorted": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.genome_bam_sorted.bam`. ", - "help_text": "Type: `file`, default: `$id.$key.genome_bam_sorted.bam`. " - , - "default": "$id.$key.genome_bam_sorted.bam" - } - - - , - "genome_bam_index": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.genome_bam_index.bai`. ", - "help_text": "Type: `file`, default: `$id.$key.genome_bam_index.bai`. " - , - "default": "$id.$key.genome_bam_index.bai" - } - - - , - "genome_bam_stats": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.genome_bam_stats.stats`. ", - "help_text": "Type: `file`, default: `$id.$key.genome_bam_stats.stats`. " - , - "default": "$id.$key.genome_bam_stats.stats" - } - - - , - "genome_bam_flagstat": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.genome_bam_flagstat.flagstat`. ", - "help_text": "Type: `file`, default: `$id.$key.genome_bam_flagstat.flagstat`. " - , - "default": "$id.$key.genome_bam_flagstat.flagstat" - } - - - , - "genome_bam_idxstats": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.genome_bam_idxstats.idxstats`. ", - "help_text": "Type: `file`, default: `$id.$key.genome_bam_idxstats.idxstats`. " - , - "default": "$id.$key.genome_bam_idxstats.idxstats" - } - - - , - "transcriptome_bam": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.transcriptome_bam.bam`. ", - "help_text": "Type: `file`, default: `$id.$key.transcriptome_bam.bam`. " - , - "default": "$id.$key.transcriptome_bam.bam" - } - - - , - "transcriptome_bam_index": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.transcriptome_bam_index.bai`. ", - "help_text": "Type: `file`, default: `$id.$key.transcriptome_bam_index.bai`. " - , - "default": "$id.$key.transcriptome_bam_index.bai" - } - - - , - "transcriptome_bam_stats": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.transcriptome_bam_stats.stats`. ", - "help_text": "Type: `file`, default: `$id.$key.transcriptome_bam_stats.stats`. " - , - "default": "$id.$key.transcriptome_bam_stats.stats" - } - - - , - "transcriptome_bam_flagstat": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.transcriptome_bam_flagstat.flagstat`. ", - "help_text": "Type: `file`, default: `$id.$key.transcriptome_bam_flagstat.flagstat`. " - , - "default": "$id.$key.transcriptome_bam_flagstat.flagstat" - } - - - , - "transcriptome_bam_idxstats": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.transcriptome_bam_idxstats.idxstats`. ", - "help_text": "Type: `file`, default: `$id.$key.transcriptome_bam_idxstats.idxstats`. " - , - "default": "$id.$key.transcriptome_bam_idxstats.idxstats" - } - - - , - "salmon_quant_results": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.salmon_quant_results.salmon_quant_results`. ", - "help_text": "Type: `file`, default: `$id.$key.salmon_quant_results.salmon_quant_results`. " - , - "default": "$id.$key.salmon_quant_results.salmon_quant_results" - } - - - , - "tpm_gene": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.tpm_gene.tsv`. ", - "help_text": "Type: `file`, default: `$id.$key.tpm_gene.tsv`. " - , - "default": "$id.$key.tpm_gene.tsv" - } - - - , - "counts_gene": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.counts_gene.tsv`. ", - "help_text": "Type: `file`, default: `$id.$key.counts_gene.tsv`. " - , - "default": "$id.$key.counts_gene.tsv" - } - - - , - "counts_gene_length_scaled": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.counts_gene_length_scaled.tsv`. ", - "help_text": "Type: `file`, default: `$id.$key.counts_gene_length_scaled.tsv`. " - , - "default": "$id.$key.counts_gene_length_scaled.tsv" - } - - - , - "counts_gene_scaled": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.counts_gene_scaled.tsv`. ", - "help_text": "Type: `file`, default: `$id.$key.counts_gene_scaled.tsv`. " - , - "default": "$id.$key.counts_gene_scaled.tsv" - } - - - , - "tpm_transcript": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.tpm_transcript.tsv`. ", - "help_text": "Type: `file`, default: `$id.$key.tpm_transcript.tsv`. " - , - "default": "$id.$key.tpm_transcript.tsv" - } - - - , - "counts_transcript": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.counts_transcript.tsv`. ", - "help_text": "Type: `file`, default: `$id.$key.counts_transcript.tsv`. " - , - "default": "$id.$key.counts_transcript.tsv" - } - - - , - "salmon_merged_summarizedexperiment": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.salmon_merged_summarizedexperiment.salmon_merged_summarizedexperiment`. ", - "help_text": "Type: `file`, default: `$id.$key.salmon_merged_summarizedexperiment.salmon_merged_summarizedexperiment`. " - , - "default": "$id.$key.salmon_merged_summarizedexperiment.salmon_merged_summarizedexperiment" - } - - - , - "markduplicates_metrics": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.markduplicates_metrics.txt`. ", - "help_text": "Type: `file`, default: `$id.$key.markduplicates_metrics.txt`. " - , - "default": "$id.$key.markduplicates_metrics.txt" - } - - - , - "stringtie_transcript_gtf": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.stringtie_transcript_gtf.gtf`. ", - "help_text": "Type: `file`, default: `$id.$key.stringtie_transcript_gtf.gtf`. " - , - "default": "$id.$key.stringtie_transcript_gtf.gtf" - } - - - , - "stringtie_coverage_gtf": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.stringtie_coverage_gtf.gtf`. ", - "help_text": "Type: `file`, default: `$id.$key.stringtie_coverage_gtf.gtf`. " - , - "default": "$id.$key.stringtie_coverage_gtf.gtf" - } - - - , - "stringtie_abundance": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.stringtie_abundance.txt`. ", - "help_text": "Type: `file`, default: `$id.$key.stringtie_abundance.txt`. " - , - "default": "$id.$key.stringtie_abundance.txt" - } - - - , - "stringtie_ballgown": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.stringtie_ballgown.ballgown`. ", - "help_text": "Type: `file`, default: `$id.$key.stringtie_ballgown.ballgown`. " - , - "default": "$id.$key.stringtie_ballgown.ballgown" - } - - - , - "featurecounts": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.featurecounts.txt`. ", - "help_text": "Type: `file`, default: `$id.$key.featurecounts.txt`. " - , - "default": "$id.$key.featurecounts.txt" - } - - - , - "featurecounts_summary": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.featurecounts_summary.summary`. ", - "help_text": "Type: `file`, default: `$id.$key.featurecounts_summary.summary`. " - , - "default": "$id.$key.featurecounts_summary.summary" - } - - - , - "featurecounts_multiqc": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.featurecounts_multiqc.tsv`. ", - "help_text": "Type: `file`, default: `$id.$key.featurecounts_multiqc.tsv`. " - , - "default": "$id.$key.featurecounts_multiqc.tsv" - } - - - , - "featurecounts_rrna_multiqc": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.featurecounts_rrna_multiqc.tsv`. ", - "help_text": "Type: `file`, default: `$id.$key.featurecounts_rrna_multiqc.tsv`. " - , - "default": "$id.$key.featurecounts_rrna_multiqc.tsv" - } - - - , - "bedgraph_forward": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.bedgraph_forward.bedgraph`. ", - "help_text": "Type: `file`, default: `$id.$key.bedgraph_forward.bedgraph`. " - , - "default": "$id.$key.bedgraph_forward.bedgraph" - } - - - , - "bedgraph_reverse": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.bedgraph_reverse.bedgraph`. ", - "help_text": "Type: `file`, default: `$id.$key.bedgraph_reverse.bedgraph`. " - , - "default": "$id.$key.bedgraph_reverse.bedgraph" - } - - - , - "bigwig_forward": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.bigwig_forward.bigwig`. ", - "help_text": "Type: `file`, default: `$id.$key.bigwig_forward.bigwig`. " - , - "default": "$id.$key.bigwig_forward.bigwig" - } - - - , - "bigwig_reverse": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.bigwig_reverse.bigwig`. ", - "help_text": "Type: `file`, default: `$id.$key.bigwig_reverse.bigwig`. " - , - "default": "$id.$key.bigwig_reverse.bigwig" - } - - - , - "preseq_output": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.preseq_output.txt`. ", - "help_text": "Type: `file`, default: `$id.$key.preseq_output.txt`. " - , - "default": "$id.$key.preseq_output.txt" - } - - - , - "bamstat_output": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.bamstat_output.txt`. Path to output file (txt) of mapping quality statistics", - "help_text": "Type: `file`, default: `$id.$key.bamstat_output.txt`. Path to output file (txt) of mapping quality statistics" - , - "default": "$id.$key.bamstat_output.txt" - } - - - , - "strandedness_output": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.strandedness_output.txt`. Path to output report (txt) of inferred strandedness", - "help_text": "Type: `file`, default: `$id.$key.strandedness_output.txt`. Path to output report (txt) of inferred strandedness" - , - "default": "$id.$key.strandedness_output.txt" - } - - - , - "inner_dist_output_stats": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.inner_dist_output_stats.stats`. output file (txt) with summary statistics of inner distances of paired reads", - "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_stats.stats`. output file (txt) with summary statistics of inner distances of paired reads" - , - "default": "$id.$key.inner_dist_output_stats.stats" - } - - - , - "inner_dist_output_dist": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.inner_dist_output_dist.txt`. output file (txt) with inner distances of all paired reads", - "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_dist.txt`. output file (txt) with inner distances of all paired reads" - , - "default": "$id.$key.inner_dist_output_dist.txt" - } - - - , - "inner_dist_output_freq": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.inner_dist_output_freq.txt`. output file (txt) with frequencies of inner distances of all paired reads", - "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_freq.txt`. output file (txt) with frequencies of inner distances of all paired reads" - , - "default": "$id.$key.inner_dist_output_freq.txt" - } - - - , - "inner_dist_output_plot": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.inner_dist_output_plot.pdf`. output file (pdf) with histogram plot of of inner distances of all paired reads", - "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_plot.pdf`. output file (pdf) with histogram plot of of inner distances of all paired reads" - , - "default": "$id.$key.inner_dist_output_plot.pdf" - } - - - , - "inner_dist_output_plot_r": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.inner_dist_output_plot_r.r`. output file (R) with script of histogram plot of of inner distances of all paired reads", - "help_text": "Type: `file`, default: `$id.$key.inner_dist_output_plot_r.r`. output file (R) with script of histogram plot of of inner distances of all paired reads" - , - "default": "$id.$key.inner_dist_output_plot_r.r" - } - - - , - "junction_annotation_output_log": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.junction_annotation_output_log.log`. output log of junction annotation script", - "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_log.log`. output log of junction annotation script" - , - "default": "$id.$key.junction_annotation_output_log.log" - } - - - , - "junction_annotation_output_plot_r": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.junction_annotation_output_plot_r.r`. R script to generate splice_junction and splice_events plot", - "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_plot_r.r`. R script to generate splice_junction and splice_events plot" - , - "default": "$id.$key.junction_annotation_output_plot_r.r" - } - - - , - "junction_annotation_output_junction_bed": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_bed.bed`. junction annotation file (bed format)", - "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_bed.bed`. junction annotation file (bed format)" - , - "default": "$id.$key.junction_annotation_output_junction_bed.bed" - } - - - , - "junction_annotation_output_junction_interact": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_interact.bed`. interact file (bed format) of junctions", - "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_interact.bed`. interact file (bed format) of junctions. Can be uploaded to UCSC genome browser or converted to bigInteract (using bedToBigBed program) for visualization." - , - "default": "$id.$key.junction_annotation_output_junction_interact.bed" - } - - - , - "junction_annotation_output_junction_sheet": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_sheet.xls`. junction annotation file (xls format)", - "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_junction_sheet.xls`. junction annotation file (xls format)" - , - "default": "$id.$key.junction_annotation_output_junction_sheet.xls" - } - - - , - "junction_annotation_output_splice_events_plot": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.junction_annotation_output_splice_events_plot.pdf`. plot of splice events (pdf)", - "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_splice_events_plot.pdf`. plot of splice events (pdf)" - , - "default": "$id.$key.junction_annotation_output_splice_events_plot.pdf" - } - - - , - "junction_annotation_output_splice_junctions_plot": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.junction_annotation_output_splice_junctions_plot.pdf`. plot of junctions (pdf)", - "help_text": "Type: `file`, default: `$id.$key.junction_annotation_output_splice_junctions_plot.pdf`. plot of junctions (pdf)" - , - "default": "$id.$key.junction_annotation_output_splice_junctions_plot.pdf" - } - - - , - "junction_saturation_output_plot_r": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.junction_saturation_output_plot_r.r`. r script to generate junction_saturation_plot plot", - "help_text": "Type: `file`, default: `$id.$key.junction_saturation_output_plot_r.r`. r script to generate junction_saturation_plot plot" - , - "default": "$id.$key.junction_saturation_output_plot_r.r" - } - - - , - "junction_saturation_output_plot": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.junction_saturation_output_plot.pdf`. plot of junction saturation (pdf", - "help_text": "Type: `file`, default: `$id.$key.junction_saturation_output_plot.pdf`. plot of junction saturation (pdf" - , - "default": "$id.$key.junction_saturation_output_plot.pdf" - } - - - , - "read_distribution_output": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.read_distribution_output.txt`. output file (txt) of read distribution analysis", - "help_text": "Type: `file`, default: `$id.$key.read_distribution_output.txt`. output file (txt) of read distribution analysis." - , - "default": "$id.$key.read_distribution_output.txt" - } - - - , - "read_duplication_output_duplication_rate_plot_r": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_plot_r.r`. R script for generating duplication rate plot", - "help_text": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_plot_r.r`. R script for generating duplication rate plot" - , - "default": "$id.$key.read_duplication_output_duplication_rate_plot_r.r" - } - - - , - "read_duplication_output_duplication_rate_plot": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_plot.pdf`. duplication rate plot (pdf)", - "help_text": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_plot.pdf`. duplication rate plot (pdf)" - , - "default": "$id.$key.read_duplication_output_duplication_rate_plot.pdf" - } - - - , - "read_duplication_output_duplication_rate_mapping": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_mapping.xls`. Summary of mapping-based read duplication", - "help_text": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_mapping.xls`. Summary of mapping-based read duplication" - , - "default": "$id.$key.read_duplication_output_duplication_rate_mapping.xls" - } - - - , - "read_duplication_output_duplication_rate_sequence": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_sequence.xls`. Summary of sequencing-based read duplication", - "help_text": "Type: `file`, default: `$id.$key.read_duplication_output_duplication_rate_sequence.xls`. Summary of sequencing-based read duplication" - , - "default": "$id.$key.read_duplication_output_duplication_rate_sequence.xls" - } - - - , - "tin_output_summary": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.tin_output_summary.txt`. summary statistics (txt) of calculated TIN metrics", - "help_text": "Type: `file`, default: `$id.$key.tin_output_summary.txt`. summary statistics (txt) of calculated TIN metrics" - , - "default": "$id.$key.tin_output_summary.txt" - } - - - , - "tin_output_metrics": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.tin_output_metrics.xls`. file with TIN metrics (xls)", - "help_text": "Type: `file`, default: `$id.$key.tin_output_metrics.xls`. file with TIN metrics (xls)" - , - "default": "$id.$key.tin_output_metrics.xls" - } - - - , - "dupradar_output_dupmatrix": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.dupradar_output_dupmatrix.txt`. path to output file (txt) of duplicate tag counts", - "help_text": "Type: `file`, default: `$id.$key.dupradar_output_dupmatrix.txt`. path to output file (txt) of duplicate tag counts" - , - "default": "$id.$key.dupradar_output_dupmatrix.txt" - } - - - , - "dupradar_output_dup_intercept_mqc": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.dupradar_output_dup_intercept_mqc.txt`. path to output file (txt) of multiqc intercept value DupRadar", - "help_text": "Type: `file`, default: `$id.$key.dupradar_output_dup_intercept_mqc.txt`. path to output file (txt) of multiqc intercept value DupRadar" - , - "default": "$id.$key.dupradar_output_dup_intercept_mqc.txt" - } - - - , - "dupradar_output_duprate_exp_boxplot": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_boxplot.pdf`. path to output file (pdf) of distribution of expression box plot", - "help_text": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_boxplot.pdf`. path to output file (pdf) of distribution of expression box plot" - , - "default": "$id.$key.dupradar_output_duprate_exp_boxplot.pdf" - } - - - , - "dupradar_output_duprate_exp_densplot": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_densplot.pdf`. path to output file (pdf) of 2D density scatter plot of duplicate tag counts", - "help_text": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_densplot.pdf`. path to output file (pdf) of 2D density scatter plot of duplicate tag counts" - , - "default": "$id.$key.dupradar_output_duprate_exp_densplot.pdf" - } - - - , - "dupradar_output_duprate_exp_denscurve_mqc": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_denscurve_mqc.pdf`. path to output file (pdf) of density curve of gene duplication multiqc", - "help_text": "Type: `file`, default: `$id.$key.dupradar_output_duprate_exp_denscurve_mqc.pdf`. path to output file (pdf) of density curve of gene duplication multiqc" - , - "default": "$id.$key.dupradar_output_duprate_exp_denscurve_mqc.pdf" - } - - - , - "dupradar_output_expression_histogram": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.dupradar_output_expression_histogram.pdf`. path to output file (pdf) of distribution of RPK values per gene histogram", - "help_text": "Type: `file`, default: `$id.$key.dupradar_output_expression_histogram.pdf`. path to output file (pdf) of distribution of RPK values per gene histogram" - , - "default": "$id.$key.dupradar_output_expression_histogram.pdf" - } - - - , - "dupradar_output_intercept_slope": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.dupradar_output_intercept_slope.txt`. ", - "help_text": "Type: `file`, default: `$id.$key.dupradar_output_intercept_slope.txt`. " - , - "default": "$id.$key.dupradar_output_intercept_slope.txt" - } - - - , - "qualimap_output_pdf": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.qualimap_output_pdf.pdf`. ", - "help_text": "Type: `file`, default: `$id.$key.qualimap_output_pdf.pdf`. " - , - "default": "$id.$key.qualimap_output_pdf.pdf" - } - - - , - "qualimap_output_dir": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.qualimap_output_dir.qualimap_output_dir`. ", - "help_text": "Type: `file`, default: `$id.$key.qualimap_output_dir.qualimap_output_dir`. " - , - "default": "$id.$key.qualimap_output_dir.qualimap_output_dir" - } - - - , - "deseq2_output": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.deseq2_output.deseq2_output`. ", - "help_text": "Type: `file`, default: `$id.$key.deseq2_output.deseq2_output`. " - , - "default": "$id.$key.deseq2_output.deseq2_output" - } - - - , - "multiqc_report": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.multiqc_report.html`. ", - "help_text": "Type: `file`, default: `$id.$key.multiqc_report.html`. " - , - "default": "$id.$key.multiqc_report.html" - } - - - , - "multiqc_data": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.multiqc_data.multiqc_data`. ", - "help_text": "Type: `file`, default: `$id.$key.multiqc_data.multiqc_data`. " - , - "default": "$id.$key.multiqc_data.multiqc_data" - } - - - , - "multiqc_plots": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.multiqc_plots.multiqc_plots`. ", - "help_text": "Type: `file`, default: `$id.$key.multiqc_plots.multiqc_plots`. " - , - "default": "$id.$key.multiqc_plots.multiqc_plots" - } - - - , - "multiqc_versions": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.multiqc_versions.multiqc_versions`. ", - "help_text": "Type: `file`, default: `$id.$key.multiqc_versions.multiqc_versions`. " - , - "default": "$id.$key.multiqc_versions.multiqc_versions" - } - - - , - "versions": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.versions.versions`. ", - "help_text": "Type: `file`, default: `$id.$key.versions.versions`. " - , - "default": "$id.$key.versions.versions" - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/input" - }, - - { - "$ref": "#/definitions/reference genome options" - }, - - { - "$ref": "#/definitions/read trimming options" - }, - - { - "$ref": "#/definitions/read filtering options" - }, - - { - "$ref": "#/definitions/umi options" - }, - - { - "$ref": "#/definitions/alignment options" - }, - - { - "$ref": "#/definitions/process skipping options" - }, - - { - "$ref": "#/definitions/other process arguments" - }, - - { - "$ref": "#/definitions/multiqc paramenters" - }, - - { - "$ref": "#/definitions/output" - }, - - { - "$ref": "#/definitions/nextflow input-output arguments" - } -] -}