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Build branch main with version main (cb9b328)

Browse Source 
Build pipeline: viash-hub.rnaseq.main-mf5kg

Source commit: cb9b328834

Source message: Update pointers to biobox and craftbox
This commit is contained in:
CI
2024-09-13 11:32:59 +00:00
parent 1ebb61f1e8
commit 92b5a42360
284 changed files with 1310 additions and 29225 deletions
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24
target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml
View File

@@ -398,26 +398,32 @@ dependencies:
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
- name: "samtools/samtools_sort"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
- name: "samtools/samtools_index"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
- name: "samtools/samtools_stats"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
- name: "samtools/samtools_flagstat"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
- name: "samtools/samtools_idxstats"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
- name: "umitools/umitools_dedup"
repository:
type: "local"
@@ -428,6 +434,7 @@ dependencies:
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
- name: "rsem/rsem_calculate_expression"
repository:
type: "local"
@@ -435,6 +442,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
runners:
- type: "executable"
id: "executable"
@@ -510,18 +518,18 @@ 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: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
git_remote: "https://github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/nextflow/star/star_align_reads"
- "target/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_sort"
- "target/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_index"
- "target/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_stats"
- "target/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_flagstat"
- "target/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_idxstats"
- "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"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats"
- "target/nextflow/umitools/umitools_dedup"
- "target/nextflow/umitools_prepareforquant"
- "target/dependencies/vsh/vsh/biobox/nextflow/salmon/salmon_quant"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
- "target/nextflow/rsem/rsem_calculate_expression"
package_config:
version: "main"

14
target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant
View File

@@ -1169,13 +1169,13 @@ fi
VIASH_DEP_UMITOOLS_UMITOOLS_DEDUP="$VIASH_META_RESOURCES_DIR/../../../nextflow/umitools/umitools_dedup/main.nf"
VIASH_DEP_UMITOOLS_PREPAREFORQUANT="$VIASH_META_RESOURCES_DIR/../../../nextflow/umitools_prepareforquant/main.nf"
VIASH_DEP_RSEM_RSEM_CALCULATE_EXPRESSION="$VIASH_META_RESOURCES_DIR/../../../nextflow/rsem/rsem_calculate_expression/main.nf"
VIASH_DEP_STAR_STAR_ALIGN_READS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/nextflow/star/star_align_reads/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_SORT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_sort/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_index/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_STATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_stats/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_FLAGSTAT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_flagstat/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_IDXSTATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_idxstats/main.nf"
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/nextflow/salmon/salmon_quant/main.nf"
VIASH_DEP_STAR_STAR_ALIGN_READS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_SORT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_STATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_FLAGSTAT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_IDXSTATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/main.nf"
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/main.nf"
ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD

2
target/executable/workflows/merge_quant_results/.config.vsh.yaml
View File

@@ -269,7 +269,7 @@ 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: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
git_remote: "https://github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/tx2gene"

24
target/executable/workflows/post_processing/.config.vsh.yaml
View File

@@ -369,27 +369,27 @@ dependencies:
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.1"
tag: "v0.2.0"
- name: "samtools/samtools_index"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.1"
tag: "v0.2.0"
- name: "samtools/samtools_stats"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.1"
tag: "v0.2.0"
- name: "samtools/samtools_flagstat"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.1"
tag: "v0.2.0"
- name: "samtools/samtools_idxstats"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.1"
tag: "v0.2.0"
- name: "stringtie"
repository:
type: "local"
@@ -406,7 +406,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.1"
tag: "v0.2.0"
runners:
- type: "executable"
id: "executable"
@@ -482,15 +482,15 @@ build_info:
output: "target/executable/workflows/post_processing"
executable: "target/executable/workflows/post_processing/post_processing"
viash_version: "0.9.0"
git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
git_remote: "https://github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/picard_markduplicates"
- "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_sort"
- "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_index"
- "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_stats"
- "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_flagstat"
- "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_idxstats"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats"
- "target/nextflow/stringtie"
- "target/nextflow/bedtools_genomecov"
- "target/nextflow/ucsc/bedclip"

10
target/executable/workflows/post_processing/post_processing
View File

@@ -1143,11 +1143,11 @@ VIASH_DEP_STRINGTIE="$VIASH_META_RESOURCES_DIR/../../../nextflow/stringtie/main.
VIASH_DEP_BEDTOOLS_GENOMECOV="$VIASH_META_RESOURCES_DIR/../../../nextflow/bedtools_genomecov/main.nf"
VIASH_DEP_UCSC_BEDCLIP="$VIASH_META_RESOURCES_DIR/../../../nextflow/ucsc/bedclip/main.nf"
VIASH_DEP_UCSC_BEDGRAPHTOBIGWIG="$VIASH_META_RESOURCES_DIR/../../../nextflow/ucsc/bedgraphtobigwig/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_SORT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_sort/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_index/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_STATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_stats/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_FLAGSTAT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_flagstat/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_IDXSTATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_idxstats/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_SORT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_STATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_FLAGSTAT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_IDXSTATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/main.nf"
ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD

12
target/executable/workflows/pre_processing/.config.vsh.yaml
View File

@@ -551,7 +551,7 @@ dependencies:
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.1"
tag: "v0.2.0"
- name: "fq_subsample"
repository:
type: "local"
@@ -559,12 +559,12 @@ dependencies:
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.1"
tag: "v0.2.0"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.1"
tag: "v0.2.0"
runners:
- type: "executable"
id: "executable"
@@ -640,7 +640,7 @@ build_info:
output: "target/executable/workflows/pre_processing"
executable: "target/executable/workflows/pre_processing/pre_processing"
viash_version: "0.9.0"
git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
git_remote: "https://github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/fastqc"
@@ -648,9 +648,9 @@ build_info:
- "target/nextflow/trimgalore"
- "target/nextflow/bbmap_bbsplit"
- "target/nextflow/sortmerna"
- "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/fastp"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp"
- "target/nextflow/fq_subsample"
- "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/salmon/salmon_quant"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
package_config:
version: "main"
info:

4
target/executable/workflows/pre_processing/pre_processing
View File

@@ -1462,8 +1462,8 @@ VIASH_DEP_TRIMGALORE="$VIASH_META_RESOURCES_DIR/../../../nextflow/trimgalore/mai
VIASH_DEP_BBMAP_BBSPLIT="$VIASH_META_RESOURCES_DIR/../../../nextflow/bbmap_bbsplit/main.nf"
VIASH_DEP_SORTMERNA="$VIASH_META_RESOURCES_DIR/../../../nextflow/sortmerna/main.nf"
VIASH_DEP_FQ_SUBSAMPLE="$VIASH_META_RESOURCES_DIR/../../../nextflow/fq_subsample/main.nf"
VIASH_DEP_FASTP="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/fastp/main.nf"
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/salmon/salmon_quant/main.nf"
VIASH_DEP_FASTP="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/main.nf"
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/main.nf"
ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD

26
target/executable/workflows/prepare_genome/.config.vsh.yaml
View File

@@ -370,7 +370,7 @@ dependencies:
repository:
type: "vsh"
repo: "biobox"
tag: "main"
tag: "v0.2.0"
- name: "cat_additional_fasta"
repository:
type: "local"
@@ -387,7 +387,7 @@ dependencies:
repository:
type: "vsh"
repo: "biobox"
tag: "main"
tag: "v0.2.0"
- name: "getchromsizes"
repository:
type: "local"
@@ -395,12 +395,12 @@ dependencies:
repository:
type: "vsh"
repo: "craftbox"
tag: "main"
tag: "v0.1.0"
- name: "star/star_genome_generate"
repository:
type: "vsh"
repo: "biobox"
tag: "main"
tag: "v0.2.0"
- name: "bbmap_bbsplit"
repository:
type: "local"
@@ -408,7 +408,7 @@ dependencies:
repository:
type: "vsh"
repo: "biobox"
tag: "main"
tag: "v0.2.0"
- name: "kallisto/kallisto_index"
repository:
type: "local"
@@ -416,11 +416,11 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "biobox"
tag: "main"
tag: "v0.2.0"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
tag: "main"
tag: "v0.1.0"
runners:
- type: "executable"
id: "executable"
@@ -496,21 +496,21 @@ build_info:
output: "target/executable/workflows/prepare_genome"
executable: "target/executable/workflows/prepare_genome/prepare_genome"
viash_version: "0.9.0"
git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
git_remote: "https://github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/gunzip"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/gffread"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread"
- "target/nextflow/cat_additional_fasta"
- "target/nextflow/gtf2bed"
- "target/nextflow/preprocess_transcripts_fasta"
- "target/nextflow/gtf_filter"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference"
- "target/nextflow/getchromsizes"
- "target/dependencies/vsh/vsh/craftbox/main/nextflow/untar"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate"
- "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/untar"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate"
- "target/nextflow/bbmap_bbsplit"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index"
- "target/nextflow/kallisto/kallisto_index"
package_config:
version: "main"

10
target/executable/workflows/prepare_genome/prepare_genome
View File

@@ -1111,11 +1111,11 @@ VIASH_DEP_GTF_FILTER="$VIASH_META_RESOURCES_DIR/../../../nextflow/gtf_filter/mai
VIASH_DEP_GETCHROMSIZES="$VIASH_META_RESOURCES_DIR/../../../nextflow/getchromsizes/main.nf"
VIASH_DEP_BBMAP_BBSPLIT="$VIASH_META_RESOURCES_DIR/../../../nextflow/bbmap_bbsplit/main.nf"
VIASH_DEP_KALLISTO_KALLISTO_INDEX="$VIASH_META_RESOURCES_DIR/../../../nextflow/kallisto/kallisto_index/main.nf"
VIASH_DEP_GFFREAD="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/gffread/main.nf"
VIASH_DEP_RSEM_RSEM_PREPARE_REFERENCE="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/main.nf"
VIASH_DEP_UNTAR="$VIASH_TARGET_DIR/dependencies/vsh/vsh/craftbox/main/nextflow/untar/main.nf"
VIASH_DEP_STAR_STAR_GENOME_GENERATE="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/main.nf"
VIASH_DEP_SALMON_SALMON_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/main.nf"
VIASH_DEP_GFFREAD="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/main.nf"
VIASH_DEP_RSEM_RSEM_PREPARE_REFERENCE="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/main.nf"
VIASH_DEP_UNTAR="$VIASH_TARGET_DIR/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/untar/main.nf"
VIASH_DEP_STAR_STAR_GENOME_GENERATE="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/main.nf"
VIASH_DEP_SALMON_SALMON_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/main.nf"
ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD

8
target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml
View File

@@ -197,7 +197,7 @@ dependencies:
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.1"
tag: "v0.2.0"
- name: "kallisto/kallisto_quant"
repository:
type: "local"
@@ -205,7 +205,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.1"
tag: "v0.2.0"
runners:
- type: "executable"
id: "executable"
@@ -281,10 +281,10 @@ 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: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
git_remote: "https://github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/salmon/salmon_quant"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
- "target/nextflow/kallisto/kallisto_quant"
package_config:
version: "main"

2
target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant
View File

@@ -784,7 +784,7 @@ fi
# set dependency paths
VIASH_DEP_KALLISTO_KALLISTO_QUANT="$VIASH_META_RESOURCES_DIR/../../../nextflow/kallisto/kallisto_quant/main.nf"
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/salmon/salmon_quant/main.nf"
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/main.nf"
ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD

12
target/executable/workflows/quality_control/.config.vsh.yaml
View File

@@ -1490,7 +1490,7 @@ dependencies:
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.1"
tag: "v0.2.0"
- name: "multiqc_custom_biotype"
repository:
type: "local"
@@ -1504,7 +1504,7 @@ dependencies:
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.1"
tag: "v0.2.0"
- name: "workflows/merge_quant_results"
repository:
type: "local"
@@ -1512,7 +1512,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.1"
tag: "v0.2.0"
runners:
- type: "executable"
id: "executable"
@@ -1588,7 +1588,7 @@ build_info:
output: "target/executable/workflows/quality_control"
executable: "target/executable/workflows/quality_control/quality_control"
viash_version: "0.9.0"
git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
git_remote: "https://github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/rseqc/rseqc_bamstat"
@@ -1602,11 +1602,11 @@ build_info:
- "target/nextflow/dupradar"
- "target/nextflow/qualimap"
- "target/nextflow/preseq_lcextrap"
- "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/featurecounts"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts"
- "target/nextflow/multiqc_custom_biotype"
- "target/nextflow/deseq2_qc"
- "target/nextflow/prepare_multiqc_input"
- "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/multiqc"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc"
- "target/nextflow/workflows/merge_quant_results"
package_config:
version: "main"

4
target/executable/workflows/quality_control/quality_control
View File

@@ -3343,8 +3343,8 @@ VIASH_DEP_MULTIQC_CUSTOM_BIOTYPE="$VIASH_META_RESOURCES_DIR/../../../nextflow/mu
VIASH_DEP_DESEQ2_QC="$VIASH_META_RESOURCES_DIR/../../../nextflow/deseq2_qc/main.nf"
VIASH_DEP_PREPARE_MULTIQC_INPUT="$VIASH_META_RESOURCES_DIR/../../../nextflow/prepare_multiqc_input/main.nf"
VIASH_DEP_WORKFLOWS_MERGE_QUANT_RESULTS="$VIASH_META_RESOURCES_DIR/../../../nextflow/workflows/merge_quant_results/main.nf"
VIASH_DEP_FEATURECOUNTS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/featurecounts/main.nf"
VIASH_DEP_MULTIQC="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/multiqc/main.nf"
VIASH_DEP_FEATURECOUNTS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/main.nf"
VIASH_DEP_MULTIQC="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf"
ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD

2
target/executable/workflows/rnaseq/.config.vsh.yaml
View File

@@ -1956,7 +1956,7 @@ build_info:
output: "target/executable/workflows/rnaseq"
executable: "target/executable/workflows/rnaseq/rnaseq"
viash_version: "0.9.0"
git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
git_remote: "https://github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/workflows/prepare_genome"