Merge branch 'master' into tool/bamtools-split

2024-09-21 07:42:05 +00:00 · 2022-04-22 19:36:18 +02:00 · 2022-04-22 19:36:18 +02:00 · c3f13fdaf6
commit c3f13fdaf6
parent da56a2d509 9957689568
12 changed files with 32 additions and 35 deletions
--- a/modules/cat/fastq/main.nf
+++ b/modules/cat/fastq/main.nf
@ -4,8 +4,8 @@ process CAT_FASTQ {

    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
    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' :
-        'biocontainers/biocontainers:v1.2.0_cv1' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"

    input:
    tuple val(meta), path(reads, stageAs: "input*/*")
--- a/modules/gunzip/main.nf
+++ b/modules/gunzip/main.nf
@ -4,8 +4,8 @@ process GUNZIP {

    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
    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' :
-        'biocontainers/biocontainers:v1.2.0_cv1' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"

    input:
    tuple val(meta), path(archive)
--- a/modules/phantompeakqualtools/main.nf
+++ b/modules/phantompeakqualtools/main.nf
@ -26,7 +26,7 @@ process PHANTOMPEAKQUALTOOLS {
    def prefix = task.ext.prefix ?: "${meta.id}"
    """
    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
    "${task.process}":
--- a/modules/stringtie/merge/main.nf
+++ b/modules/stringtie/merge/main.nf
@ -2,10 +2,10 @@ process STRINGTIE_MERGE {
    label 'process_medium'

    // 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 ?
-        'https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0' :
-        'quay.io/biocontainers/stringtie:2.1.7--h978d192_0' }"
+        'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' :
+        'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }"

    input:
    path stringtie_gtf
--- a/modules/stringtie/stringtie/main.nf
+++ b/modules/stringtie/stringtie/main.nf
@ -1,11 +1,11 @@
-process STRINGTIE {
+process STRINGTIE_STRINGTIE {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0' :
-        'quay.io/biocontainers/stringtie:2.1.7--h978d192_0' }"
+        'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' :
+        'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }"

    input:
    tuple val(meta), path(bam)
--- a/modules/stringtie/stringtie/meta.yml
+++ b/modules/stringtie/stringtie/meta.yml
@ -1,4 +1,4 @@
-name: stringtie
+name: stringtie_stringtie
 description: Transcript assembly and quantification for RNA-Se
 keywords:
  - transcript
--- a/modules/untar/main.nf
+++ b/modules/untar/main.nf
@ -2,10 +2,10 @@ process UNTAR {
    tag "$archive"
    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 ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' :
-        'biocontainers/biocontainers:v1.2.0_cv2' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"

    input:
    tuple val(meta), path(archive)
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@ -335,6 +335,7 @@ params {
        'bacteroides_fragilis' {
            'genome' {
                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                      = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf"
                genome_mapping_potential_arg    = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.mapping.potential.ARG"

--- a/tests/modules/stringtie/merge/main.nf
+++ b/tests/modules/stringtie/merge/main.nf
@ -2,8 +2,8 @@

 nextflow.enable.dsl = 2

-include { STRINGTIE       } from '../../../../modules/stringtie/stringtie/main.nf'
-include { STRINGTIE_MERGE } from '../../../../modules/stringtie/merge/main.nf'
+include { STRINGTIE_STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
+include { STRINGTIE_MERGE     } from '../../../../modules/stringtie/merge/main.nf'

 /*
 * Test with forward strandedness
@ -15,8 +15,8 @@ workflow test_stringtie_forward_merge {
    ]
    annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)

-    STRINGTIE ( input, annotation_gtf )
-    STRINGTIE
+    STRINGTIE_STRINGTIE ( input, annotation_gtf )
+    STRINGTIE_STRINGTIE
        .out
        .transcript_gtf
        .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)

-    STRINGTIE ( input, annotation_gtf )
-    STRINGTIE
+    STRINGTIE_STRINGTIE ( input, annotation_gtf )
+    STRINGTIE_STRINGTIE
        .out
        .transcript_gtf
        .map { it -> it[1] }
--- a/tests/modules/stringtie/merge/test.yml
+++ b/tests/modules/stringtie/merge/test.yml
@ -5,7 +5,7 @@
    - stringtie/merge
  files:
    - path: output/stringtie/stringtie.merged.gtf
-      md5sum: 9fab7049ef2eafdea246fc787d1def40
+      md5sum: d959eb2fab0db48ded7275e0a2e83c05
    - path: output/stringtie/test.ballgown/e2t.ctab
      md5sum: 9ae42e056c955a88a883e5e917840d77
    - path: output/stringtie/test.ballgown/e_data.ctab
@ -17,11 +17,10 @@
    - path: output/stringtie/test.ballgown/t_data.ctab
      md5sum: 92a98902784e7406ffe054d2adbabc7c
    - path: output/stringtie/test.coverage.gtf
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: output/stringtie/test.gene.abundance.txt
-      md5sum: 9708811bcefe0f6384293d6f419f3250
+      md5sum: 8bcd8e2730ed3337e2730186dbc184f3
    - path: output/stringtie/test.transcripts.gtf
-      md5sum: 0e42709bfe30c2c7f2574ba664f5fa9f
+      md5sum: a914bd55b68a4b5f607738b17861e362

 - 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
@ -30,7 +29,7 @@
    - stringtie/merge
  files:
    - path: output/stringtie/stringtie.merged.gtf
-      md5sum: afc461bb3cbc368f268a7a45c1b54497
+      md5sum: 6da479298d73d5b3216d4e1576a2bdf4
    - path: output/stringtie/test.ballgown/e2t.ctab
      md5sum: 9ae42e056c955a88a883e5e917840d77
    - path: output/stringtie/test.ballgown/e_data.ctab
@ -42,8 +41,7 @@
    - path: output/stringtie/test.ballgown/t_data.ctab
      md5sum: 92a98902784e7406ffe054d2adbabc7c
    - path: output/stringtie/test.coverage.gtf
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: output/stringtie/test.gene.abundance.txt
-      md5sum: 94b85145d60ab1b80a7f0f6cf08418b0
+      md5sum: f289f41b3ba1b9f0aa05d14408f1a5da
    - path: output/stringtie/test.transcripts.gtf
-      md5sum: 3196e3d50fd461aae6408e0a70acae68
+      md5sum: 9dcdc9577c0fdbb25089eda210267546
--- a/tests/modules/stringtie/stringtie/main.nf
+++ b/tests/modules/stringtie/stringtie/main.nf
@ -2,7 +2,7 @@

 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
 //
@ -13,7 +13,7 @@ workflow test_stringtie_forward {
    ]
    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)

-    STRINGTIE ( input, annotation_gtf )
+    STRINGTIE_STRINGTIE ( input, annotation_gtf )
 }
--- a/tests/modules/stringtie/stringtie/test.yml
+++ b/tests/modules/stringtie/stringtie/test.yml
@ -8,7 +8,6 @@
    - path: ./output/stringtie/test.gene.abundance.txt
      md5sum: 7d8bce7f2a922e367cedccae7267c22e
    - path: ./output/stringtie/test.coverage.gtf
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: ./output/stringtie/test.ballgown/e_data.ctab
      md5sum: 6b4cf69bc03f3f69890f972a0e8b7471
    - path: ./output/stringtie/test.ballgown/i_data.ctab
@ -30,7 +29,6 @@
    - path: ./output/stringtie/test.gene.abundance.txt
      md5sum: 7385b870b955dae2c2ab78a70cf05cce
    - path: ./output/stringtie/test.coverage.gtf
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: ./output/stringtie/test.ballgown/e_data.ctab
      md5sum: 879b6696029d19c4737b562e9d149218
    - path: ./output/stringtie/test.ballgown/i_data.ctab