Merge branch 'master' into tool/bamtools-split

This commit is contained in:
Matthias De Smet 2022-04-22 19:36:18 +02:00 committed by GitHub
commit c3f13fdaf6
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12 changed files with 32 additions and 35 deletions

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@ -4,8 +4,8 @@ process CAT_FASTQ {
conda (params.enable_conda ? "conda-forge::sed=4.7" : null) conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' : 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'biocontainers/biocontainers:v1.2.0_cv1' }" 'ubuntu:20.04' }"
input: input:
tuple val(meta), path(reads, stageAs: "input*/*") tuple val(meta), path(reads, stageAs: "input*/*")

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@ -4,8 +4,8 @@ process GUNZIP {
conda (params.enable_conda ? "conda-forge::sed=4.7" : null) conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' : 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'biocontainers/biocontainers:v1.2.0_cv1' }" 'ubuntu:20.04' }"
input: input:
tuple val(meta), path(archive) tuple val(meta), path(archive)

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@ -26,7 +26,7 @@ process PHANTOMPEAKQUALTOOLS {
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
RUN_SPP=`which run_spp.R` RUN_SPP=`which run_spp.R`
Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out"
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

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@ -2,10 +2,10 @@ process STRINGTIE_MERGE {
label 'process_medium' label 'process_medium'
// Note: 2.7X indices incompatible with AWS iGenomes. // Note: 2.7X indices incompatible with AWS iGenomes.
conda (params.enable_conda ? "bioconda::stringtie=2.1.7" : null) conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0' : 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' :
'quay.io/biocontainers/stringtie:2.1.7--h978d192_0' }" 'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }"
input: input:
path stringtie_gtf path stringtie_gtf

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@ -1,11 +1,11 @@
process STRINGTIE { process STRINGTIE_STRINGTIE {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::stringtie=2.1.7" : null) conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0' : 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' :
'quay.io/biocontainers/stringtie:2.1.7--h978d192_0' }" 'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

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@ -1,4 +1,4 @@
name: stringtie name: stringtie_stringtie
description: Transcript assembly and quantification for RNA-Se description: Transcript assembly and quantification for RNA-Se
keywords: keywords:
- transcript - transcript

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@ -2,10 +2,10 @@ process UNTAR {
tag "$archive" tag "$archive"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "conda-forge::tar=1.34" : null) conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' : 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'biocontainers/biocontainers:v1.2.0_cv2' }" 'ubuntu:20.04' }"
input: input:
tuple val(meta), path(archive) tuple val(meta), path(archive)

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@ -335,6 +335,7 @@ params {
'bacteroides_fragilis' { 'bacteroides_fragilis' {
'genome' { 'genome' {
genome_fna_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz" genome_fna_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz"
genome_gbff_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz"
genome_paf = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf" genome_paf = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf"
genome_mapping_potential_arg = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.mapping.potential.ARG" genome_mapping_potential_arg = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.mapping.potential.ARG"

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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf' include { STRINGTIE_STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
include { STRINGTIE_MERGE } from '../../../../modules/stringtie/merge/main.nf' include { STRINGTIE_MERGE } from '../../../../modules/stringtie/merge/main.nf'
/* /*
@ -15,8 +15,8 @@ workflow test_stringtie_forward_merge {
] ]
annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE ( input, annotation_gtf ) STRINGTIE_STRINGTIE ( input, annotation_gtf )
STRINGTIE STRINGTIE_STRINGTIE
.out .out
.transcript_gtf .transcript_gtf
.map { it -> it[1] } .map { it -> it[1] }
@ -35,8 +35,8 @@ workflow test_stringtie_reverse_merge {
] ]
annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE ( input, annotation_gtf ) STRINGTIE_STRINGTIE ( input, annotation_gtf )
STRINGTIE STRINGTIE_STRINGTIE
.out .out
.transcript_gtf .transcript_gtf
.map { it -> it[1] } .map { it -> it[1] }

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@ -5,7 +5,7 @@
- stringtie/merge - stringtie/merge
files: files:
- path: output/stringtie/stringtie.merged.gtf - path: output/stringtie/stringtie.merged.gtf
md5sum: 9fab7049ef2eafdea246fc787d1def40 md5sum: d959eb2fab0db48ded7275e0a2e83c05
- path: output/stringtie/test.ballgown/e2t.ctab - path: output/stringtie/test.ballgown/e2t.ctab
md5sum: 9ae42e056c955a88a883e5e917840d77 md5sum: 9ae42e056c955a88a883e5e917840d77
- path: output/stringtie/test.ballgown/e_data.ctab - path: output/stringtie/test.ballgown/e_data.ctab
@ -17,11 +17,10 @@
- path: output/stringtie/test.ballgown/t_data.ctab - path: output/stringtie/test.ballgown/t_data.ctab
md5sum: 92a98902784e7406ffe054d2adbabc7c md5sum: 92a98902784e7406ffe054d2adbabc7c
- path: output/stringtie/test.coverage.gtf - path: output/stringtie/test.coverage.gtf
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/stringtie/test.gene.abundance.txt - path: output/stringtie/test.gene.abundance.txt
md5sum: 9708811bcefe0f6384293d6f419f3250 md5sum: 8bcd8e2730ed3337e2730186dbc184f3
- path: output/stringtie/test.transcripts.gtf - path: output/stringtie/test.transcripts.gtf
md5sum: 0e42709bfe30c2c7f2574ba664f5fa9f md5sum: a914bd55b68a4b5f607738b17861e362
- name: stringtie merge test_stringtie_reverse_merge - name: stringtie merge test_stringtie_reverse_merge
command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config
@ -30,7 +29,7 @@
- stringtie/merge - stringtie/merge
files: files:
- path: output/stringtie/stringtie.merged.gtf - path: output/stringtie/stringtie.merged.gtf
md5sum: afc461bb3cbc368f268a7a45c1b54497 md5sum: 6da479298d73d5b3216d4e1576a2bdf4
- path: output/stringtie/test.ballgown/e2t.ctab - path: output/stringtie/test.ballgown/e2t.ctab
md5sum: 9ae42e056c955a88a883e5e917840d77 md5sum: 9ae42e056c955a88a883e5e917840d77
- path: output/stringtie/test.ballgown/e_data.ctab - path: output/stringtie/test.ballgown/e_data.ctab
@ -42,8 +41,7 @@
- path: output/stringtie/test.ballgown/t_data.ctab - path: output/stringtie/test.ballgown/t_data.ctab
md5sum: 92a98902784e7406ffe054d2adbabc7c md5sum: 92a98902784e7406ffe054d2adbabc7c
- path: output/stringtie/test.coverage.gtf - path: output/stringtie/test.coverage.gtf
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/stringtie/test.gene.abundance.txt - path: output/stringtie/test.gene.abundance.txt
md5sum: 94b85145d60ab1b80a7f0f6cf08418b0 md5sum: f289f41b3ba1b9f0aa05d14408f1a5da
- path: output/stringtie/test.transcripts.gtf - path: output/stringtie/test.transcripts.gtf
md5sum: 3196e3d50fd461aae6408e0a70acae68 md5sum: 9dcdc9577c0fdbb25089eda210267546

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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf' include { STRINGTIE_STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
// //
// Test with forward strandedness // Test with forward strandedness
// //
@ -13,7 +13,7 @@ workflow test_stringtie_forward {
] ]
annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE ( input, annotation_gtf ) STRINGTIE_STRINGTIE ( input, annotation_gtf )
} }
// //
@ -26,5 +26,5 @@ workflow test_stringtie_reverse {
] ]
annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
STRINGTIE ( input, annotation_gtf ) STRINGTIE_STRINGTIE ( input, annotation_gtf )
} }

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@ -8,7 +8,6 @@
- path: ./output/stringtie/test.gene.abundance.txt - path: ./output/stringtie/test.gene.abundance.txt
md5sum: 7d8bce7f2a922e367cedccae7267c22e md5sum: 7d8bce7f2a922e367cedccae7267c22e
- path: ./output/stringtie/test.coverage.gtf - path: ./output/stringtie/test.coverage.gtf
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: ./output/stringtie/test.ballgown/e_data.ctab - path: ./output/stringtie/test.ballgown/e_data.ctab
md5sum: 6b4cf69bc03f3f69890f972a0e8b7471 md5sum: 6b4cf69bc03f3f69890f972a0e8b7471
- path: ./output/stringtie/test.ballgown/i_data.ctab - path: ./output/stringtie/test.ballgown/i_data.ctab
@ -30,7 +29,6 @@
- path: ./output/stringtie/test.gene.abundance.txt - path: ./output/stringtie/test.gene.abundance.txt
md5sum: 7385b870b955dae2c2ab78a70cf05cce md5sum: 7385b870b955dae2c2ab78a70cf05cce
- path: ./output/stringtie/test.coverage.gtf - path: ./output/stringtie/test.coverage.gtf
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: ./output/stringtie/test.ballgown/e_data.ctab - path: ./output/stringtie/test.ballgown/e_data.ctab
md5sum: 879b6696029d19c4737b562e9d149218 md5sum: 879b6696029d19c4737b562e9d149218
- path: ./output/stringtie/test.ballgown/i_data.ctab - path: ./output/stringtie/test.ballgown/i_data.ctab