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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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25
target/executable/workflows/prepare_genome/.config.vsh.yaml
View File

@@ -370,7 +370,7 @@ dependencies:
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- name: "cat_additional_fasta"
repository:
type: "local"
@@ -387,7 +387,7 @@ dependencies:
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- name: "getchromsizes"
repository:
type: "local"
@@ -400,7 +400,7 @@ dependencies:
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- name: "bbmap_bbsplit"
repository:
type: "local"
@@ -408,7 +408,7 @@ dependencies:
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- name: "kallisto/kallisto_index"
repository:
type: "local"
@@ -416,7 +416,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -496,23 +496,24 @@ build_info:
output: "target/executable/workflows/prepare_genome"
executable: "target/executable/workflows/prepare_genome/prepare_genome"
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/nextflow/gunzip"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/gffread"
- "target/nextflow/cat_additional_fasta"
- "target/nextflow/gtf2bed"
- "target/nextflow/preprocess_transcripts_fasta"
- "target/nextflow/gtf_filter"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference"
- "target/nextflow/getchromsizes"
- "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/untar"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate"
- "target/nextflow/bbmap_bbsplit"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index"
- "target/nextflow/kallisto/kallisto_index"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -522,7 +523,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

8
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="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/main.nf"
VIASH_DEP_RSEM_RSEM_PREPARE_REFERENCE="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/main.nf"
VIASH_DEP_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="$VIASH_TARGET_DIR/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/untar/main.nf"
VIASH_DEP_STAR_STAR_GENOME_GENERATE="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/main.nf"
VIASH_DEP_SALMON_SALMON_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/main.nf"
VIASH_DEP_STAR_STAR_GENOME_GENERATE="$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"
ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD