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Build branch main with version main (05d48ac)

Browse Source 
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
This commit is contained in:
CI
2024-10-25 09:08:46 +00:00
parent 54557aa596
commit fe41adb0c7
298 changed files with 3125 additions and 3983 deletions
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37
target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml
View File

@@ -479,32 +479,32 @@ dependencies:
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- name: "samtools/samtools_sort"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- name: "samtools/samtools_index"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- name: "samtools/samtools_stats"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- name: "samtools/samtools_flagstat"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- name: "samtools/samtools_idxstats"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- name: "umitools/umitools_dedup"
repository:
type: "local"
@@ -515,7 +515,7 @@ dependencies:
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- name: "rsem/rsem_calculate_expression"
repository:
type: "local"
@@ -523,7 +523,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -603,20 +603,21 @@ 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: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@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"
- "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/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats"
- "target/nextflow/umitools/umitools_dedup"
- "target/nextflow/umitools_prepareforquant"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant"
- "target/nextflow/rsem/rsem_calculate_expression"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -626,7 +627,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

19
target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant
View File

@@ -1323,13 +1323,13 @@ 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/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"
VIASH_DEP_STAR_STAR_ALIGN_READS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_SORT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_STATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_FLAGSTAT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf"
VIASH_DEP_SAMTOOLS_SAMTOOLS_IDXSTATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf"
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf"
ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD
@@ -1644,7 +1644,7 @@ workflow run_wf {
"paired": "paired",
"input": "input",
"index": "rsem_index",
"extra_args": "extra_args"
"extra_args": "extra_rsem_calculate_expression_args"
],
toState: [
"rsem_counts_gene": "counts_gene",
@@ -1710,8 +1710,7 @@ workflow run_wf {
}
| setState (
[ "star_alignment": "star_alignment",
"star_multiqc": "star_multiqc",
[ "star_multiqc": "star_multiqc",
"rsem_multiqc": "rsem_multiqc",
"salmon_multiqc": "salmon_multiqc",
"genome_bam_sorted": "genome_bam_sorted",