CI
fe41adb0c7
Build pipeline: viash-hub.rnaseq.main-c7sdt
Source commit: 05d48ac2f8
Source message: Multiple fixes (#26)
* unset argument if not paired
* fix argument name
* add count_read_pairs argument
* output star log
* move biotypes header file into multiqc_custom_biotype component
* move deseq2 header files into deseq2_qc component
* update output defaults
* use biobox main
* add parameters to example
* update component
* update component
* ribo database processing moved to workflow
* clean code, remove unused arguments
41 lines
2.4 KiB
YAML
41 lines
2.4 KiB
YAML
param_list:
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- id: WT_REP1
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fastq_1:
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- https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/testdata/GSE110004/SRR6357070_1.fastq.gz
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- https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/testdata/GSE110004/SRR6357071_1.fastq.gz
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fastq_2:
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- https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/testdata/GSE110004/SRR6357070_2.fastq.gz
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- https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/testdata/GSE110004/SRR6357071_2.fastq.gz
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strandedness: reverse
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- id: WT_REP2
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fastq_1:
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- https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/testdata/GSE110004/SRR6357072_1.fastq.gz
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fastq_2:
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- https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/testdata/GSE110004/SRR6357072_2.fastq.gz
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strandedness: reverse
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- id: RAP1_IAA_30M_REP1
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fastq_1:
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- https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/testdata/GSE110004/SRR6357076_1.fastq.gz
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fastq_2:
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- https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/testdata/GSE110004/SRR6357076_2.fastq.gz
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strandedness: reverse
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- id: RAP1_UNINDUCED_REP1
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fastq_1:
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- https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/testdata/GSE110004/SRR6357073_1.fastq.gz
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strandedness: reverse
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- id: RAP1_UNINDUCED_REP2
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fastq_1:
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- https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/testdata/GSE110004/SRR6357074_1.fastq.gz
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- https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/testdata/GSE110004/SRR6357075_1.fastq.gz
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strandedness: reverse
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fasta: https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/reference/genome.fasta
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gtf: https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/reference/genes.gtf.gz
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additional_fasta: https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/reference/gfp.fa.gz
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transcript_fasta: https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/reference/transcriptome.fasta
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bbsplit_fasta_list: https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/reference/bbsplit_fasta_list.txt
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salmon_index: https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/reference/salmon.tar.gz
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skip_bbsplit: true
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multiqc_custom_config: https://raw.githubusercontent.com/viash-hub/rnaseq/refs/heads/main/src/assets/multiqc_config.yml
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multiqc_methods_description: https://raw.githubusercontent.com/viash-hub/rnaseq/refs/heads/main/src/assets/methods_description_template.yml
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