mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 05:13:09 +00:00
nf-core modules bump-versions for all modules (#630)
* Add blacklist of modules that shouldn't be updated to .nf-core.yml * nf-core modules bump-versions for all modules * Remove TODO statements identified by linting * Fix md5sums for failing tests * Fix more tests
This commit is contained in:
Harshil Patel
GitHub
parent
e1951d54be
commit
c5235a983d
96 changed files with 321 additions and 347 deletions
9
.nf-core.yml
Normal file
9
.nf-core.yml
Normal file
|
|
@ -0,0 +1,9 @@
|
|||
bump-versions:
|
||||
rseqc/junctionannotation: False
|
||||
rseqc/bamstat: False
|
||||
rseqc/readduplication: False
|
||||
rseqc/readdistribution: False
|
||||
rseqc/junctionsaturation: False
|
||||
rseqc/inferexperiment: False
|
||||
rseqc/innerdistance: False
|
||||
sortmerna: False
|
||||
|
|
@ -11,11 +11,11 @@ process ALLELECOUNTER {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::cancerit-allelecount=4.2.1" : null)
|
||||
conda (params.enable_conda ? 'bioconda::cancerit-allelecount=4.3.0' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.2.1--h3ecb661_0"
|
||||
container "https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.3.0--h41abebc_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/cancerit-allelecount:4.2.1--h3ecb661_0"
|
||||
container "quay.io/biocontainers/cancerit-allelecount:4.3.0--h41abebc_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process BCFTOOLS_CONSENSUS {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.11' : null)
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container 'https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0'
|
||||
container 'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0'
|
||||
} else {
|
||||
container 'quay.io/biocontainers/bcftools:1.11--h7c999a4_0'
|
||||
container 'quay.io/biocontainers/bcftools:1.13--h3a49de5_0'
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process BCFTOOLS_FILTER {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
|
||||
container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process BCFTOOLS_ISEC {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
|
||||
container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process BCFTOOLS_MERGE {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
|
||||
container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process BCFTOOLS_MPILEUP {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
|
||||
container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process BCFTOOLS_STATS {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
|
||||
container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
|
||||
container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process BLAST_BLASTN {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::blast=2.10.1' : null)
|
||||
conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container 'https://depot.galaxyproject.org/singularity/blast:2.10.1--pl526he19e7b1_3'
|
||||
container 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0'
|
||||
} else {
|
||||
container 'quay.io/biocontainers/blast:2.10.1--pl526he19e7b1_3'
|
||||
container 'quay.io/biocontainers/blast:2.12.0--pl5262h3289130_0'
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process BLAST_MAKEBLASTDB {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::blast=2.10.1' : null)
|
||||
conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container 'https://depot.galaxyproject.org/singularity/blast:2.10.1--pl526he19e7b1_3'
|
||||
container 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0'
|
||||
} else {
|
||||
container 'quay.io/biocontainers/blast:2.10.1--pl526he19e7b1_3'
|
||||
container 'quay.io/biocontainers/blast:2.12.0--pl5262h3289130_0'
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process BOWTIE2_BUILD {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::bowtie2=2.4.2' : null)
|
||||
conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.2--py38h1c8e9b9_1'
|
||||
container 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0'
|
||||
} else {
|
||||
container 'quay.io/biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1'
|
||||
container 'quay.io/biocontainers/bowtie2:2.4.4--py36hd4290be_0'
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process CNVKIT {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::cnvkit=0.9.8" : null)
|
||||
conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/cnvkit:0.9.8--py_0"
|
||||
container "https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/cnvkit:0.9.8--py_0"
|
||||
container "quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process CUTADAPT {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::cutadapt=3.2' : null)
|
||||
conda (params.enable_conda ? 'bioconda::cutadapt=3.4' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container 'https://depot.galaxyproject.org/singularity/cutadapt:3.2--py38h0213d0e_0'
|
||||
container 'https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1'
|
||||
} else {
|
||||
container 'quay.io/biocontainers/cutadapt:3.2--py38h0213d0e_0'
|
||||
container 'quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1'
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process DEEPTOOLS_COMPUTEMATRIX {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null)
|
||||
conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0"
|
||||
container "https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/deeptools:3.5.0--py_0"
|
||||
container "quay.io/biocontainers/deeptools:3.5.1--py_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process DEEPTOOLS_PLOTFINGERPRINT {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null)
|
||||
conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0"
|
||||
container "https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/deeptools:3.5.0--py_0"
|
||||
container "quay.io/biocontainers/deeptools:3.5.1--py_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process DEEPTOOLS_PLOTHEATMAP {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null)
|
||||
conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0"
|
||||
container "https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/deeptools:3.5.0--py_0"
|
||||
container "quay.io/biocontainers/deeptools:3.5.1--py_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process DEEPTOOLS_PLOTPROFILE {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::deeptools=3.5.0" : null)
|
||||
conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0"
|
||||
container "https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/deeptools:3.5.0--py_0"
|
||||
container "quay.io/biocontainers/deeptools:3.5.1--py_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -10,11 +10,11 @@ process GUBBINS {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gubbins=2.4.1" : null)
|
||||
conda (params.enable_conda ? 'bioconda::gubbins=3.0.0' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/gubbins:2.4.1--py38h197edbe_1"
|
||||
container "https://depot.galaxyproject.org/singularity/gubbins:3.0.0--py39h5bf99c6_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/gubbins:2.4.1--py38h197edbe_1"
|
||||
container "quay.io/biocontainers/gubbins:3.0.0--py39h5bf99c6_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -14,11 +14,11 @@ process HISAT2_BUILD {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
|
||||
conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
|
||||
container "https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3"
|
||||
} else {
|
||||
container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
|
||||
container "quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -13,11 +13,11 @@ process HISAT2_EXTRACTSPLICESITES {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
|
||||
conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
|
||||
container "https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3"
|
||||
} else {
|
||||
container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
|
||||
container "quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process IQTREE {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::iqtree=2.1.2" : null)
|
||||
conda (params.enable_conda ? 'bioconda::iqtree=2.1.4_beta' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/iqtree:2.1.2--h56fc30b_0"
|
||||
container "https://depot.galaxyproject.org/singularity/iqtree:2.1.4_beta--hdcc8f71_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/iqtree:2.1.2--h56fc30b_0"
|
||||
container "quay.io/biocontainers/iqtree:2.1.4_beta--hdcc8f71_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,47 +11,45 @@ process KALLISTOBUSTOOLS_COUNT {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::kb-python=0.26.0" : null)
|
||||
conda (params.enable_conda ? 'bioconda::kb-python=0.26.3' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/kb-python:0.26.0--pyhdfd78af_0"
|
||||
container "https://depot.galaxyproject.org/singularity/kb-python:0.26.3--pyhdfd78af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/kb-python:0.26.0--pyhdfd78af_0"
|
||||
container "quay.io/biocontainers/kb-python:0.26.3--pyhdfd78af_0"
|
||||
}
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path index
|
||||
path t2g
|
||||
path t1c
|
||||
path t2c
|
||||
val use_t1c
|
||||
val use_t2c
|
||||
val workflow
|
||||
val technology
|
||||
tuple val(meta), path(reads)
|
||||
path index
|
||||
path t2g
|
||||
path t1c
|
||||
path t2c
|
||||
val workflow
|
||||
val technology
|
||||
|
||||
output:
|
||||
tuple val(meta), path ("*_kallistobustools_count") , emit: kallistobustools_count
|
||||
path "*.version.txt" , emit: version
|
||||
tuple val(meta), path ("*.count"), emit: count
|
||||
path "*.version.txt" , emit: version
|
||||
|
||||
script:
|
||||
def software = getSoftwareName(task.process)
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def cdna = use_t1c ? "-c1 $t1c" : ''
|
||||
def introns = use_t2c ? "-c2 $t2c" : ''
|
||||
def cdna = t1c ? "-c1 $t1c" : ''
|
||||
def introns = t2c ? "-c2 $t2c" : ''
|
||||
"""
|
||||
kb \\
|
||||
count \\
|
||||
-t $task.cpus \\
|
||||
-i $index \\
|
||||
-g $t2g \\
|
||||
$cdna \\
|
||||
$introns \\
|
||||
--workflow $workflow \\
|
||||
-x $technology \\
|
||||
$options.args \\
|
||||
-o ${prefix}_kallistobustools_count \\
|
||||
${reads[0]} \\
|
||||
${reads[1]}
|
||||
count \\
|
||||
-t $task.cpus \\
|
||||
-i $index \\
|
||||
-g $t2g \\
|
||||
$cdna \\
|
||||
$introns \\
|
||||
--workflow $workflow \\
|
||||
-x $technology \\
|
||||
$options.args \\
|
||||
-o ${prefix}.count \\
|
||||
${reads[0]} \\
|
||||
${reads[1]}
|
||||
|
||||
echo \$(kb 2>&1) | sed 's/^kb_python //; s/Usage.*\$//' > ${software}.version.txt
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -18,14 +18,11 @@ input:
|
|||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fastq1:
|
||||
type: file
|
||||
description: Read 1 fastq file
|
||||
pattern: "*.{fastq,fastq.gz}"
|
||||
- fastq2:
|
||||
type: file
|
||||
description: Read 2 fastq file
|
||||
pattern: "*.{fastq,fastq.gz}"
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- index:
|
||||
type: file
|
||||
description: kb-ref index file (.idx)
|
||||
|
|
@ -38,17 +35,11 @@ input:
|
|||
type: file
|
||||
description: kb ref's c1 spliced_t2c file
|
||||
pattern: "*.{cdna_t2c.txt}"
|
||||
- use_t1c:
|
||||
type: boolean
|
||||
description: Whether to use the c1 txt file for RNA velocity and nucleus workflows
|
||||
- t2c:
|
||||
type: file
|
||||
description: kb ref's c2 unspliced_t2c file
|
||||
pattern: "*.{introns_t2c.txt}"
|
||||
- use_t2c:
|
||||
type: boolean
|
||||
description: Whether to use the c2 txt file for RNA velocity and nucleus workflows
|
||||
- kb_workflow:
|
||||
- workflow:
|
||||
type: value
|
||||
description: String value defining worfklow to use, can be one of "standard", "lamanno", "nucleus"
|
||||
pattern: "{standard,lamanno,nucleus,kite}"
|
||||
|
|
@ -57,17 +48,16 @@ input:
|
|||
description: String value defining the sequencing technology used.
|
||||
pattern: "{10XV1,10XV2,10XV3,CELSEQ,CELSEQ2,DROPSEQ,INDROPSV1,INDROPSV2,INDROPSV3,SCRUBSEQ,SURECELL,SMARTSEQ}"
|
||||
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test']
|
||||
- kallistobustools_count:
|
||||
- count:
|
||||
type: file
|
||||
description: kb count output folder
|
||||
pattern: "*_{kallistobustools_count}"
|
||||
pattern: "*.{count}"
|
||||
- version:
|
||||
type: file
|
||||
description: File containing software version
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process KALLISTOBUSTOOLS_REF {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::kb-python=0.26.0" : null)
|
||||
conda (params.enable_conda ? 'bioconda::kb-python=0.26.3' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/kb-python:0.26.0--pyhdfd78af_0"
|
||||
container "https://depot.galaxyproject.org/singularity/kb-python:0.26.3--pyhdfd78af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/kb-python:0.26.0--pyhdfd78af_0"
|
||||
container "quay.io/biocontainers/kb-python:0.26.3--pyhdfd78af_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process LAST_DOTPLOT {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::last=1238" : null)
|
||||
conda (params.enable_conda ? 'bioconda::last=1250' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
|
||||
container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/last:1238--h2e03b76_0"
|
||||
container "quay.io/biocontainers/last:1250--h2e03b76_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process LAST_LASTAL {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::last=1238" : null)
|
||||
conda (params.enable_conda ? 'bioconda::last=1250' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
|
||||
container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/last:1238--h2e03b76_0"
|
||||
container "quay.io/biocontainers/last:1250--h2e03b76_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process LAST_LASTDB {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::last=1238" : null)
|
||||
conda (params.enable_conda ? 'bioconda::last=1250' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
|
||||
container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/last:1238--h2e03b76_0"
|
||||
container "quay.io/biocontainers/last:1250--h2e03b76_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process LAST_MAFCONVERT {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::last=1238" : null)
|
||||
conda (params.enable_conda ? 'bioconda::last=1250' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
|
||||
container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/last:1238--h2e03b76_0"
|
||||
container "quay.io/biocontainers/last:1250--h2e03b76_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process LAST_MAFSWAP {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::last=1238" : null)
|
||||
conda (params.enable_conda ? 'bioconda::last=1250' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
|
||||
container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/last:1238--h2e03b76_0"
|
||||
container "quay.io/biocontainers/last:1250--h2e03b76_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process LAST_POSTMASK {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::last=1238" : null)
|
||||
conda (params.enable_conda ? 'bioconda::last=1250' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
|
||||
container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/last:1238--h2e03b76_0"
|
||||
container "quay.io/biocontainers/last:1250--h2e03b76_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process LAST_SPLIT {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::last=1238" : null)
|
||||
conda (params.enable_conda ? 'bioconda::last=1250' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
|
||||
container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/last:1238--h2e03b76_0"
|
||||
container "quay.io/biocontainers/last:1250--h2e03b76_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process LAST_TRAIN {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::last=1238" : null)
|
||||
conda (params.enable_conda ? 'bioconda::last=1250' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
|
||||
container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/last:1238--h2e03b76_0"
|
||||
container "quay.io/biocontainers/last:1250--h2e03b76_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process METAPHLAN3 {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::metaphlan=3.0.10" : null)
|
||||
conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/metaphlan:3.0.10--pyhb7b1952_0"
|
||||
container "https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/metaphlan:3.0.10--pyhb7b1952_0"
|
||||
container "quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process METHYLDACKEL_EXTRACT {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::methyldackel=0.5.2" : null)
|
||||
conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/methyldackel:0.5.2--h7435645_0"
|
||||
container "https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/methyldackel:0.5.2--h7435645_0"
|
||||
container "quay.io/biocontainers/methyldackel:0.6.0--h22771d5_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process METHYLDACKEL_MBIAS {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::methyldackel=0.5.2" : null)
|
||||
conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/methyldackel:0.5.2--h7435645_0"
|
||||
container "https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/methyldackel:0.5.2--h7435645_0"
|
||||
container "quay.io/biocontainers/methyldackel:0.6.0--h22771d5_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process MINIMAP2_ALIGN {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::minimap2=2.17" : null)
|
||||
conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/minimap2:2.17--hed695b0_3"
|
||||
container "https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/minimap2:2.17--hed695b0_3"
|
||||
container "quay.io/biocontainers/minimap2:2.21--h5bf99c6_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -10,11 +10,11 @@ process MINIMAP2_INDEX {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:['']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::minimap2=2.17" : null)
|
||||
conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/minimap2:2.17--hed695b0_3"
|
||||
container "https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/minimap2:2.17--hed695b0_3"
|
||||
container "quay.io/biocontainers/minimap2:2.21--h5bf99c6_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process MOSDEPTH {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::mosdepth=0.3.1' : null)
|
||||
conda (params.enable_conda ? 'bioconda::mosdepth=0.3.2' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/mosdepth:0.3.1--ha7ba039_0"
|
||||
container "https://depot.galaxyproject.org/singularity/mosdepth:0.3.2--h01d7912_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/mosdepth:0.3.1--ha7ba039_0"
|
||||
container "quay.io/biocontainers/mosdepth:0.3.2--h01d7912_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -10,11 +10,11 @@ process MULTIQC {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::multiqc=1.10.1" : null)
|
||||
conda (params.enable_conda ? 'bioconda::multiqc=1.11' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/multiqc:1.10.1--py_0"
|
||||
container "https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/multiqc:1.10.1--py_0"
|
||||
container "quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process NANOPLOT {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::nanoplot=1.36.1" : null)
|
||||
conda (params.enable_conda ? 'bioconda::nanoplot=1.38.0' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/nanoplot:1.36.1--pyhdfd78af_0"
|
||||
container "https://depot.galaxyproject.org/singularity/nanoplot:1.38.0--pyhdfd78af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/nanoplot:1.36.1--pyhdfd78af_0"
|
||||
container "quay.io/biocontainers/nanoplot:1.38.0--pyhdfd78af_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process PICARD_COLLECTMULTIPLEMETRICS {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.23.9" : null)
|
||||
conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/picard:2.23.9--0"
|
||||
container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/picard:2.23.9--0"
|
||||
container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process PICARD_COLLECTWGSMETRICS {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.25.0" : null)
|
||||
conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/picard:2.25.0--0"
|
||||
container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/picard:2.25.0--0"
|
||||
container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process PICARD_FILTERSAMREADS {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.25.6" : null)
|
||||
conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/picard:2.25.6--hdfd78af_0"
|
||||
container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/picard:2.25.6--hdfd78af_0"
|
||||
container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process PICARD_MARKDUPLICATES {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.23.9" : null)
|
||||
conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/picard:2.23.9--0"
|
||||
container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/picard:2.23.9--0"
|
||||
container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process PICARD_MERGESAMFILES {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.23.9" : null)
|
||||
conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/picard:2.23.9--0"
|
||||
container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/picard:2.23.9--0"
|
||||
container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -12,11 +12,11 @@ process PICARD_SORTSAM {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.25.6" : null)
|
||||
conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/picard:2.25.6--hdfd78af_0"
|
||||
container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/picard:2.25.6--hdfd78af_0"
|
||||
container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -1,32 +1,27 @@
|
|||
name: prodigal
|
||||
## TODO nf-core: Add a description of the module and list keywords
|
||||
description: write your description here
|
||||
description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program
|
||||
keywords:
|
||||
- sort
|
||||
tools:
|
||||
- prodigal:
|
||||
## TODO nf-core: Add a description and other details for the software below
|
||||
description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program
|
||||
homepage: {}
|
||||
documentation: {}
|
||||
tool_dev_url: {}
|
||||
doi: ""
|
||||
licence: ['GPL v3']
|
||||
licence: ["GPL v3"]
|
||||
|
||||
## TODO nf-core: Add a description of all of the variables used as input
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
## TODO nf-core: Delete / customise this example input
|
||||
- bam:
|
||||
type: file
|
||||
description: BAM/CRAM/SAM file
|
||||
pattern: "*.{bam,cram,sam}"
|
||||
|
||||
## TODO nf-core: Add a description of all of the variables used as output
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
|
|
@ -37,7 +32,6 @@ output:
|
|||
type: file
|
||||
description: File containing software version
|
||||
pattern: "*.{version.txt}"
|
||||
## TODO nf-core: Delete / customise this example output
|
||||
- bam:
|
||||
type: file
|
||||
description: Sorted BAM/CRAM/SAM file
|
||||
|
|
|
|||
|
|
@ -10,11 +10,11 @@ process RAXMLNG {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::raxml-ng=1.0.2" : null)
|
||||
conda (params.enable_conda ? 'bioconda::raxml-ng=1.0.3' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/raxml-ng:1.0.2--h7447c1b_0"
|
||||
container "https://depot.galaxyproject.org/singularity/raxml-ng:1.0.3--h32fcf60_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/raxml-ng:1.0.2--h7447c1b_0"
|
||||
container "quay.io/biocontainers/raxml-ng:1.0.3--h32fcf60_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process SALMON_INDEX {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null)
|
||||
conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/salmon:1.4.0--hf69c8f4_0"
|
||||
container "https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/salmon:1.4.0--hf69c8f4_0"
|
||||
container "quay.io/biocontainers/salmon:1.5.2--h84f40af_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process SALMON_QUANT {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null)
|
||||
conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/salmon:1.4.0--hf69c8f4_0"
|
||||
container "https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/salmon:1.4.0--hf69c8f4_0"
|
||||
container "quay.io/biocontainers/salmon:1.5.2--h84f40af_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process SAMTOOLS_FAIDX {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
|
||||
conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
|
||||
container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process SAMTOOLS_FASTQ {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
|
||||
conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
|
||||
container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process SAMTOOLS_FLAGSTAT {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
|
||||
conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
|
||||
container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process SAMTOOLS_IDXSTATS {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
|
||||
conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
|
||||
container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process SAMTOOLS_INDEX {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
|
||||
conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
|
||||
container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process SAMTOOLS_MERGE {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
|
||||
conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
|
||||
container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process SAMTOOLS_MPILEUP {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
|
||||
conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
|
||||
container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process SAMTOOLS_SORT {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
|
||||
conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
|
||||
container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process SAMTOOLS_STATS {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
|
||||
conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
|
||||
container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process SAMTOOLS_VIEW {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
|
||||
conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
|
||||
container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
|
||||
container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -12,12 +12,12 @@ process SEQKIT_SPLIT2 {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::seqkit=0.16.0" : null)
|
||||
conda (params.enable_conda ? 'bioconda::seqkit=0.16.1' : null)
|
||||
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/seqkit:0.16.0--h9ee0642_0"
|
||||
container "https://depot.galaxyproject.org/singularity/seqkit:0.16.1--h9ee0642_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/seqkit:0.16.0--h9ee0642_0"
|
||||
container "quay.io/biocontainers/seqkit:0.16.1--h9ee0642_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -12,12 +12,12 @@ process SEQWISH_INDUCE {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::seqwish=0.4.1" : null)
|
||||
conda (params.enable_conda ? 'bioconda::seqwish=0.7.1' : null)
|
||||
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/seqwish:0.4.1--h8b12597_0"
|
||||
container "https://depot.galaxyproject.org/singularity/seqwish:0.7.1--h2e03b76_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/seqwish:0.4.1--h8b12597_0"
|
||||
container "quay.io/biocontainers/seqwish:0.7.1--h2e03b76_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -1,5 +1,4 @@
|
|||
name: shovill
|
||||
## TODO nf-core: Add a description of the module and list keywords
|
||||
description: Assemble bacterial isolate genomes from Illumina paired-end reads
|
||||
keywords:
|
||||
- bacterial
|
||||
|
|
@ -8,11 +7,10 @@ keywords:
|
|||
|
||||
tools:
|
||||
- shovill:
|
||||
## TODO nf-core: Add a description and other details for the software below
|
||||
description: Microbial assembly pipeline for Illumina paired-end reads
|
||||
homepage: https://github.com/tseemann/shovill
|
||||
documentation: https://github.com/tseemann/shovill/blob/master/README.md
|
||||
licence: ['GPL v2']
|
||||
licence: ["GPL v2"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
@ -21,8 +19,8 @@ input:
|
|||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: List of input paired-end FastQ files
|
||||
type: file
|
||||
description: List of input paired-end FastQ files
|
||||
|
||||
output:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process SPADES {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::spades=3.15.2" : null)
|
||||
conda (params.enable_conda ? 'bioconda::spades=3.15.3' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/spades:3.15.2--h95f258a_1"
|
||||
container "https://depot.galaxyproject.org/singularity/spades:3.15.3--h95f258a_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/spades:3.15.2--h95f258a_1"
|
||||
container "quay.io/biocontainers/spades:3.15.3--h95f258a_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process TABIX_BGZIP {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::tabix=0.2.6" : null)
|
||||
conda (params.enable_conda ? 'bioconda::tabix=1.11' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/tabix:0.2.6--ha92aebf_0"
|
||||
container "https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
|
||||
container "quay.io/biocontainers/tabix:1.11--hdfd78af_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process TABIX_BGZIPTABIX {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::tabix=0.2.6" : null)
|
||||
conda (params.enable_conda ? 'bioconda::tabix=1.11' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/tabix:0.2.6--ha92aebf_0"
|
||||
container "https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
|
||||
container "quay.io/biocontainers/tabix:1.11--hdfd78af_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process TABIX_TABIX {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::tabix=0.2.6" : null)
|
||||
conda (params.enable_conda ? 'bioconda::tabix=1.11' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/tabix:0.2.6--ha92aebf_0"
|
||||
container "https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
|
||||
container "quay.io/biocontainers/tabix:1.11--hdfd78af_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ process TRIMGALORE {
|
|||
mode: params.publish_dir_mode,
|
||||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
|
||||
|
||||
conda (params.enable_conda ? "bioconda::trim-galore=0.6.6" : null)
|
||||
conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.6--0"
|
||||
container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0"
|
||||
} else {
|
||||
container "quay.io/biocontainers/trim-galore:0.6.6--0"
|
||||
container "quay.io/biocontainers/trim-galore:0.6.7--hdfd78af_0"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- bcftools
|
||||
files:
|
||||
- path: output/bcftools/test.vcf.gz
|
||||
md5sum: 9d491cfa84067450342ba8e66c75e5b8
|
||||
md5sum: fc178eb342a91dc0d1d568601ad8f8e2
|
||||
|
|
|
|||
|
|
@ -5,8 +5,8 @@
|
|||
- bcftools
|
||||
files:
|
||||
- path: output/bcftools/test.bcftools_stats.txt
|
||||
md5sum: 2d506e32837a53a01fea0fc90402632a
|
||||
md5sum: 74863ef525eef8d87e3119146d281bcf
|
||||
- path: output/bcftools/test.vcf.gz.tbi
|
||||
md5sum: 11d90b5b35e4adf6b44fc53bec93bed3
|
||||
md5sum: 0772419c5d819b4caa4aebfcad010c6e
|
||||
- path: output/bcftools/test.vcf.gz
|
||||
md5sum: 2cf273a9fa3784383799b6b24df2f88c
|
||||
md5sum: 9811674bb8da7ff30581319a910f2396
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- bcftools/stats
|
||||
files:
|
||||
- path: output/bcftools/test.bcftools_stats.txt
|
||||
md5sum: c4c5938add12a20050eec3782c8ad623
|
||||
md5sum: d3543531396cf7012f13ebdce639cbc8
|
||||
|
|
|
|||
|
|
@ -13,10 +13,10 @@
|
|||
- path: ./output/blast/blast_db/genome.fasta.nhr
|
||||
md5sum: f4b4ddb034fd3dd7b25c89e9d50c004e
|
||||
- path: ./output/blast/blast_db/genome.fasta.ndb
|
||||
md5sum: 45f2daf9769957ff80868dd3d80d30a3
|
||||
md5sum: 0d553c830656469211de113c5022f06d
|
||||
- path: ./output/blast/blast_db/genome.fasta.not
|
||||
md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
|
||||
- path: ./output/blast/blast_db/genome.fasta.nto
|
||||
md5sum: 33cdeccccebe80329f1fdbee7f5874cb
|
||||
- path: ./output/blast/blast_db/genome.fasta.ntf
|
||||
md5sum: 1f6027d443e67a98ad0edc2d39971b0c
|
||||
md5sum: de1250813f0c7affc6d12dac9d0fb6bb
|
||||
|
|
|
|||
|
|
@ -12,10 +12,10 @@
|
|||
- path: ./output/blast/blast_db/genome.fasta.nhr
|
||||
md5sum: f4b4ddb034fd3dd7b25c89e9d50c004e
|
||||
- path: ./output/blast/blast_db/genome.fasta.ndb
|
||||
md5sum: 45f2daf9769957ff80868dd3d80d30a3
|
||||
md5sum: 0d553c830656469211de113c5022f06d
|
||||
- path: ./output/blast/blast_db/genome.fasta.not
|
||||
md5sum: 1e53e9d08f1d23af0299cfa87478a7bb
|
||||
- path: ./output/blast/blast_db/genome.fasta.nto
|
||||
md5sum: 33cdeccccebe80329f1fdbee7f5874cb
|
||||
- path: ./output/blast/blast_db/genome.fasta.ntf
|
||||
md5sum: 1f6027d443e67a98ad0edc2d39971b0c
|
||||
md5sum: de1250813f0c7affc6d12dac9d0fb6bb
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@
|
|||
- path: output/deeptools/test.plotFingerprint.pdf
|
||||
- path: output/deeptools/test.plotFingerprint.qcmetrics.txt
|
||||
contains:
|
||||
- "AUC"
|
||||
- "0.24184576629880325"
|
||||
- "AUC"
|
||||
- "0.24184576629880325"
|
||||
- path: output/deeptools/test.plotFingerprint.raw.txt
|
||||
md5sum: e2a9ff341a315f49e7c8387a3323bdfb
|
||||
md5sum: aff8e53de0ddd893aa9d8f9d4ce7e291
|
||||
|
|
|
|||
|
|
@ -10,14 +10,14 @@
|
|||
- path: output/gubbins/all_sites.recombination_predictions.gff
|
||||
md5sum: f95871e79968340cb82532e2c9b0c92b
|
||||
- path: output/gubbins/all_sites.branch_base_reconstruction.embl
|
||||
md5sum: 02e6fb268f7422bfe34b27ecd3b2c245
|
||||
md5sum: 9e051646d630f528fff58f1f73286006
|
||||
- path: output/gubbins/all_sites.summary_of_snp_distribution.vcf
|
||||
md5sum: 276e62e888ea811577c8ffb2da0b3aff
|
||||
- path: output/gubbins/all_sites.per_branch_statistics.csv
|
||||
md5sum: 94b09b25d10504b56aa0307beae98a98
|
||||
md5sum: 25e4fdb6681c3709a9add1d5632bbf3e
|
||||
- path: output/gubbins/all_sites.filtered_polymorphic_sites.phylip
|
||||
md5sum: 0a77f397a7797c5c3386832745b0c97a
|
||||
- path: output/gubbins/all_sites.final_tree.tre
|
||||
md5sum: e3c7ea18e2c5c49774c0e2ff78bd1818
|
||||
md5sum: 6cb251b58307aab11cb4b48792d6cda1
|
||||
- path: output/gubbins/all_sites.node_labelled.final_tree.tre
|
||||
md5sum: 7727b4c4111ebf49cc8a4f1fdd25092c
|
||||
md5sum: e01f965a15924b4f97603b8011c8d3f7
|
||||
|
|
|
|||
|
|
@ -14,7 +14,7 @@
|
|||
- path: output/index/hisat2/genome.7.ht2
|
||||
md5sum: 9013eccd91ad614d7893c739275a394f
|
||||
- path: output/index/hisat2/genome.1.ht2
|
||||
md5sum: 3ea3dc41304941ad8d047e4d71b4899e
|
||||
md5sum: 057cfa8a22b97ee9cff4c8d342498803
|
||||
- path: output/index/hisat2/genome.2.ht2
|
||||
md5sum: 47b153cd1319abc88dda532462651fcf
|
||||
- path: output/index/hisat2/genome.6.ht2
|
||||
|
|
@ -42,7 +42,7 @@
|
|||
- path: output/index/hisat2/genome.7.ht2
|
||||
md5sum: 9013eccd91ad614d7893c739275a394f
|
||||
- path: output/index/hisat2/genome.1.ht2
|
||||
md5sum: 3ea3dc41304941ad8d047e4d71b4899e
|
||||
md5sum: 057cfa8a22b97ee9cff4c8d342498803
|
||||
- path: output/index/hisat2/genome.2.ht2
|
||||
md5sum: 47b153cd1319abc88dda532462651fcf
|
||||
- path: output/index/hisat2/genome.6.ht2
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@
|
|||
- path: output/index/hisat2/genome.7.ht2
|
||||
md5sum: 9013eccd91ad614d7893c739275a394f
|
||||
- path: output/index/hisat2/genome.1.ht2
|
||||
md5sum: 3ea3dc41304941ad8d047e4d71b4899e
|
||||
md5sum: 057cfa8a22b97ee9cff4c8d342498803
|
||||
- path: output/index/hisat2/genome.2.ht2
|
||||
md5sum: 47b153cd1319abc88dda532462651fcf
|
||||
- path: output/index/hisat2/genome.6.ht2
|
||||
|
|
|
|||
|
|
@ -5,20 +5,20 @@ nextflow.enable.dsl = 2
|
|||
include { KALLISTOBUSTOOLS_COUNT } from '../../../../modules/kallistobustools/count/main.nf' addParams( options: [args:"--cellranger"] )
|
||||
|
||||
workflow test_kallistobustools_count {
|
||||
|
||||
input = [ [id:'test_standard'], // meta map
|
||||
[file("https://github.com/nf-core/test-datasets/blob/modules/data/genomics/homo_sapiens/illumina/10xgenomics/test_1.fastq.gz?raw=true", checkIfExists: true),
|
||||
file("https://github.com/nf-core/test-datasets/blob/modules/data/genomics/homo_sapiens/illumina/10xgenomics/test_2.fastq.gz?raw=true", checkIfExists: true)]
|
||||
]
|
||||
|
||||
index = file("https://github.com/FloWuenne/test-datasets/blob/scrnaseq/reference/kallistobustools/kb_ref.idx?raw=true", checkIfExists: true)
|
||||
t2g = file("https://raw.githubusercontent.com/FloWuenne/test-datasets/scrnaseq/reference/kallistobustools/t2g.txt", checkIfExists: true)
|
||||
t1c = file('t1c_dummy')
|
||||
t2c = file('t2c_dummy')
|
||||
use_t1c = false
|
||||
use_t2c = false
|
||||
workflow = "standard"
|
||||
technology = "10XV3"
|
||||
|
||||
KALLISTOBUSTOOLS_COUNT (input,index,t2g,t1c,t2c,use_t1c,use_t2c,workflow,technology)
|
||||
input = [
|
||||
[id:'test'], // meta map
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['test_10x_1_fastq_gz'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_10x_2_fastq_gz'], checkIfExists: true)
|
||||
]
|
||||
]
|
||||
|
||||
index = file("https://github.com/FloWuenne/test-datasets/blob/scrnaseq/reference/kallistobustools/kb_ref.idx?raw=true", checkIfExists: true)
|
||||
t2g = file("https://raw.githubusercontent.com/FloWuenne/test-datasets/scrnaseq/reference/kallistobustools/t2g.txt", checkIfExists: true)
|
||||
t1c = []
|
||||
t2c = []
|
||||
workflow = "standard"
|
||||
technology = "10XV3"
|
||||
|
||||
KALLISTOBUSTOOLS_COUNT ( input, index, t2g, t1c, t2c, workflow, technology )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -4,33 +4,33 @@
|
|||
- kallistobustools/count
|
||||
- kallistobustools
|
||||
files:
|
||||
- path: output/kallistobustools/test_standard_kallistobustools_count/10xv3_whitelist.txt
|
||||
- path: output/kallistobustools/test.count/10x_version3_whitelist.txt
|
||||
md5sum: 3d36d0a4021fd292b265e2b5e72aaaf3
|
||||
- path: output/kallistobustools/test_standard_kallistobustools_count/counts_unfiltered/cellranger/barcodes.tsv
|
||||
- path: output/kallistobustools/test.count/counts_unfiltered/cellranger/barcodes.tsv
|
||||
md5sum: 8f734732c46f52c4d1c025bfe4134bd2
|
||||
- path: output/kallistobustools/test_standard_kallistobustools_count/counts_unfiltered/cellranger/genes.tsv
|
||||
- path: output/kallistobustools/test.count/counts_unfiltered/cellranger/genes.tsv
|
||||
md5sum: fbebf995a3de568db8ac028cd0c5d993
|
||||
- path: output/kallistobustools/test_standard_kallistobustools_count/counts_unfiltered/cellranger/matrix.mtx
|
||||
- path: output/kallistobustools/test.count/counts_unfiltered/cellranger/matrix.mtx
|
||||
md5sum: 4847bae27c41961496d504bcfe9890ba
|
||||
- path: output/kallistobustools/test_standard_kallistobustools_count/counts_unfiltered/cells_x_genes.barcodes.txt
|
||||
- path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.barcodes.txt
|
||||
md5sum: cafdf96423987e3d9e807cdc16139541
|
||||
- path: output/kallistobustools/test_standard_kallistobustools_count/counts_unfiltered/cells_x_genes.genes.txt
|
||||
- path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.genes.txt
|
||||
md5sum: 52d0627aaf0418bebe3ef75ad77da53f
|
||||
- path: output/kallistobustools/test_standard_kallistobustools_count/counts_unfiltered/cells_x_genes.mtx
|
||||
- path: output/kallistobustools/test.count/counts_unfiltered/cells_x_genes.mtx
|
||||
md5sum: d05e1582385ba5f215fa73c470343c06
|
||||
- path: output/kallistobustools/test_standard_kallistobustools_count/inspect.json
|
||||
- path: output/kallistobustools/test.count/inspect.json
|
||||
md5sum: d3d23063f3fc07f7fbd24748aa4271a9
|
||||
- path: output/kallistobustools/test_standard_kallistobustools_count/kb_info.json
|
||||
contains:
|
||||
- 'kallisto'
|
||||
- path: output/kallistobustools/test_standard_kallistobustools_count/matrix.ec
|
||||
- path: output/kallistobustools/test.count/kb_info.json
|
||||
contains:
|
||||
- "kallisto"
|
||||
- path: output/kallistobustools/test.count/matrix.ec
|
||||
md5sum: cd8340e3fb78d74ad85fabdbe0a778f0
|
||||
- path: output/kallistobustools/test_standard_kallistobustools_count/output.bus
|
||||
- path: output/kallistobustools/test.count/output.bus
|
||||
md5sum: f4702922bd0c142e34b3680c2251426a
|
||||
- path: output/kallistobustools/test_standard_kallistobustools_count/output.unfiltered.bus
|
||||
- path: output/kallistobustools/test.count/output.unfiltered.bus
|
||||
md5sum: e38f99748e598e33fe035b89e7c89fb5
|
||||
- path: output/kallistobustools/test_standard_kallistobustools_count/run_info.json
|
||||
contains:
|
||||
- 'n_targets'
|
||||
- path: output/kallistobustools/test_standard_kallistobustools_count/transcripts.txt
|
||||
- path: output/kallistobustools/test.count/run_info.json
|
||||
contains:
|
||||
- "n_targets"
|
||||
- path: output/kallistobustools/test.count/transcripts.txt
|
||||
md5sum: 6d583083eaf6ca81e409332a40d2e74c
|
||||
|
|
|
|||
|
|
@ -5,11 +5,8 @@
|
|||
- kallistobustools
|
||||
files:
|
||||
- path: output/kallistobustools/cdna.fa
|
||||
md5sum: 0de7fdac9e7418576987ed93640927c7
|
||||
- path: output/kallistobustools/kb_ref_out.idx
|
||||
md5sum: 7d5cd0731e7c467e5521d761f7d79895
|
||||
- path: output/kallistobustools/t2g.txt
|
||||
md5sum: d5bcfd61ff078aa92e576abf8cc4fc08
|
||||
|
||||
- name: kallistobustools ref test_kallistobustools_ref_lamanno
|
||||
command: nextflow run tests/modules/kallistobustools/ref -entry test_kallistobustools_ref_lamanno -c tests/config/nextflow.config
|
||||
|
|
@ -18,17 +15,11 @@
|
|||
- kallistobustools
|
||||
files:
|
||||
- path: output/kallistobustools/cdna.fa
|
||||
md5sum: 0de7fdac9e7418576987ed93640927c7
|
||||
- path: output/kallistobustools/cdna_t2c.txt
|
||||
md5sum: 6d583083eaf6ca81e409332a40d2e74c
|
||||
- path: output/kallistobustools/intron.fa
|
||||
md5sum: ca5ca147afa0a25f6a730edfb39a6098
|
||||
- path: output/kallistobustools/intron_t2c.txt
|
||||
md5sum: 728480007abfdbdb248f7ba9de6026ef
|
||||
- path: output/kallistobustools/kb_ref_out.idx
|
||||
md5sum: 48ca8323aadd30b1762d4e8f5a7d7aee
|
||||
- path: output/kallistobustools/t2g.txt
|
||||
md5sum: 7cae93dfb9a26f70adf4a57fe2a83027
|
||||
|
||||
- name: kallistobustools ref test_kallistobustools_ref_nucleus
|
||||
command: nextflow run tests/modules/kallistobustools/ref -entry test_kallistobustools_ref_nucleus -c tests/config/nextflow.config
|
||||
|
|
@ -37,14 +28,8 @@
|
|||
- kallistobustools
|
||||
files:
|
||||
- path: output/kallistobustools/cdna.fa
|
||||
md5sum: 0de7fdac9e7418576987ed93640927c7
|
||||
- path: output/kallistobustools/cdna_t2c.txt
|
||||
md5sum: 6d583083eaf6ca81e409332a40d2e74c
|
||||
- path: output/kallistobustools/intron.fa
|
||||
md5sum: ca5ca147afa0a25f6a730edfb39a6098
|
||||
- path: output/kallistobustools/intron_t2c.txt
|
||||
md5sum: 728480007abfdbdb248f7ba9de6026ef
|
||||
- path: output/kallistobustools/kb_ref_out.idx
|
||||
md5sum: 48ca8323aadd30b1762d4e8f5a7d7aee
|
||||
- path: output/kallistobustools/t2g.txt
|
||||
md5sum: 7cae93dfb9a26f70adf4a57fe2a83027
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
- last/lastal
|
||||
files:
|
||||
- path: output/last/contigs.genome.maf.gz
|
||||
md5sum: 2fc56553282d0826310bdef16a55e587
|
||||
md5sum: 670f4fa1a94b23690cdb6fc603813c75
|
||||
- path: output/untar/lastdb/genome.bck
|
||||
md5sum: 5519879b9b6c4d1fc508da7f17f88f2e
|
||||
- path: output/untar/lastdb/genome.des
|
||||
|
|
@ -28,7 +28,7 @@
|
|||
- last/lastal
|
||||
files:
|
||||
- path: output/last/contigs.genome.maf.gz
|
||||
md5sum: f50557bed5430b42de7b0d5d61075cf0
|
||||
md5sum: b0202b013e1caa9163516cd4ff4fbdbc
|
||||
- path: output/untar/lastdb/genome.bck
|
||||
md5sum: 5519879b9b6c4d1fc508da7f17f88f2e
|
||||
- path: output/untar/lastdb/genome.des
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@
|
|||
- path: output/last/lastdb/test.des
|
||||
md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc
|
||||
- path: output/last/lastdb/test.prj
|
||||
md5sum: 2c981eb9b9d2012d8413946a5b378f20
|
||||
md5sum: 6948d17d2a10e470ea545f659930a543
|
||||
- path: output/last/lastdb/test.sds
|
||||
md5sum: 2cd381f4f8a9c52cfcd323a2863eccb2
|
||||
- path: output/last/lastdb/test.ssp
|
||||
|
|
@ -30,7 +30,7 @@
|
|||
- path: output/last/lastdb/test.des
|
||||
md5sum: 26ab49015cc572172b9efa50fc5190bc
|
||||
- path: output/last/lastdb/test.prj
|
||||
md5sum: aec51a18da1c2361aaca70dd16eb7b7b
|
||||
md5sum: d253fc4320d9b4d7fcfc43b2734412ee
|
||||
- path: output/last/lastdb/test.sds
|
||||
md5sum: cad9927d4bd161257e98165ad755d8e4
|
||||
- path: output/last/lastdb/test.ssp
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
- minimap2/align
|
||||
files:
|
||||
- path: ./output/minimap2/test.paf
|
||||
md5sum: 5a9648fc67c30a2c83b0ef094171faa0
|
||||
md5sum: 70e8cf299ee3ecd33e629d10c1f588ce
|
||||
|
||||
- name: minimap2 align paired-end
|
||||
command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_paired_end -c tests/config/nextflow.config
|
||||
|
|
@ -14,4 +14,4 @@
|
|||
- minimap2/align
|
||||
files:
|
||||
- path: ./output/minimap2/test.paf
|
||||
md5sum: e7b952be872bdbef16bf99d512690df7
|
||||
md5sum: 5e7b55a26bf0ea3a2843423d3e0b9a28
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@
|
|||
files:
|
||||
- path: ./output/picard/test.MarkDuplicates.metrics.txt
|
||||
- path: ./output/picard/test.bam
|
||||
md5sum: fe8ed25b4bd25be0cc7a8730fc3b2f30
|
||||
md5sum: 3270bb142039e86aaf2ab83c540225d5
|
||||
|
||||
- name: picard markduplicates on unsorted bam
|
||||
command: nextflow run ./tests/modules/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- picard/mergesamfiles
|
||||
files:
|
||||
- path: ./output/picard/test.bam
|
||||
md5sum: b8bd6c22f36c6ebc91bca98bd637a2eb
|
||||
md5sum: 82bb91735aff82eae4f0b631114e9e15
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@
|
|||
- path: ./output/index/salmon/refseq.bin
|
||||
md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
|
||||
- path: ./output/index/salmon/versionInfo.json
|
||||
md5sum: 204865f645102587c4953fccb256797c
|
||||
md5sum: 6c764bd219b7bc17168a99d232c0fe09
|
||||
- path: ./output/index/salmon/complete_ref_lens.bin
|
||||
md5sum: f57562f1fca3ae7b133f895ae13c3d08
|
||||
- path: ./output/index/salmon/mphf.bin
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@
|
|||
md5sum: 687368b9963874c1797d210310b38516
|
||||
- path: ./output/salmon/test/lib_format_counts.json
|
||||
- path: ./output/salmon/test/quant.genes.sf
|
||||
md5sum: ad4d31437f06db49b2436abeec29c78e
|
||||
md5sum: af6d88f109e0d0d6a0826bdf2b3b7e97
|
||||
- path: ./output/salmon/test/logs/salmon_quant.log
|
||||
- path: ./output/salmon/test/aux_info/expected_bias.gz
|
||||
md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
|
||||
|
|
@ -27,7 +27,7 @@
|
|||
- path: ./output/index/salmon/refseq.bin
|
||||
md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
|
||||
- path: ./output/index/salmon/versionInfo.json
|
||||
md5sum: 204865f645102587c4953fccb256797c
|
||||
md5sum: 6c764bd219b7bc17168a99d232c0fe09
|
||||
- path: ./output/index/salmon/complete_ref_lens.bin
|
||||
md5sum: f57562f1fca3ae7b133f895ae13c3d08
|
||||
- path: ./output/index/salmon/mphf.bin
|
||||
|
|
@ -60,7 +60,7 @@
|
|||
md5sum: 4abd35d0a60b5279b394424f0e6ea42d
|
||||
- path: ./output/salmon/test/lib_format_counts.json
|
||||
- path: ./output/salmon/test/quant.genes.sf
|
||||
md5sum: d750f8c9f248e30c3a6d0c2678bf9c6a
|
||||
md5sum: 29c8cd26f609cacd4fb88713df9c71c2
|
||||
- path: ./output/salmon/test/logs/salmon_quant.log
|
||||
- path: ./output/salmon/test/aux_info/expected_bias.gz
|
||||
md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
|
||||
|
|
@ -78,7 +78,7 @@
|
|||
- path: ./output/index/salmon/refseq.bin
|
||||
md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
|
||||
- path: ./output/index/salmon/versionInfo.json
|
||||
md5sum: 204865f645102587c4953fccb256797c
|
||||
md5sum: 6c764bd219b7bc17168a99d232c0fe09
|
||||
- path: ./output/index/salmon/complete_ref_lens.bin
|
||||
md5sum: f57562f1fca3ae7b133f895ae13c3d08
|
||||
- path: ./output/index/salmon/mphf.bin
|
||||
|
|
@ -112,7 +112,7 @@
|
|||
md5sum: 687368b9963874c1797d210310b38516
|
||||
- path: ./output/salmon/test/lib_format_counts.json
|
||||
- path: ./output/salmon/test/quant.genes.sf
|
||||
md5sum: ad4d31437f06db49b2436abeec29c78e
|
||||
md5sum: af6d88f109e0d0d6a0826bdf2b3b7e97
|
||||
- path: ./output/salmon/test/logs/salmon_quant.log
|
||||
- path: output/salmon/test/aux_info/expected_bias.gz
|
||||
md5sum: 24ee10af39b41ecf4f4e08faaaf537ee
|
||||
|
|
@ -130,7 +130,7 @@
|
|||
- path: output/index/salmon/refseq.bin
|
||||
md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
|
||||
- path: output/index/salmon/versionInfo.json
|
||||
md5sum: 204865f645102587c4953fccb256797c
|
||||
md5sum: 6c764bd219b7bc17168a99d232c0fe09
|
||||
- path: output/index/salmon/complete_ref_lens.bin
|
||||
md5sum: f57562f1fca3ae7b133f895ae13c3d08
|
||||
- path: output/index/salmon/mphf.bin
|
||||
|
|
|
|||
|
|
@ -5,6 +5,6 @@
|
|||
- samtools/fastq
|
||||
files:
|
||||
- path: output/samtools/test_2.fastq.gz
|
||||
md5sum: 229daf1a62d114cae42c65801e8c0114
|
||||
md5sum: 3b1c92f33a44a78d82f8360ab4fdfd61
|
||||
- path: output/samtools/test_1.fastq.gz
|
||||
md5sum: 4cab81f76e66361611621377f1b69d1d
|
||||
md5sum: 5a3f9c69a032c4ffd9071ea31a14e6f9
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- samtools/flagstat
|
||||
files:
|
||||
- path: ./output/samtools/test.paired_end.sorted.bam.flagstat
|
||||
md5sum: 6d7934c303b15ce473f64d502b79984e
|
||||
md5sum: 4f7ffd1e6a5e85524d443209ac97d783
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- samtools/mpileup
|
||||
files:
|
||||
- path: ./output/samtools/test.mpileup
|
||||
md5sum: 3608af83ffe3efbb1337f0ffb205337d
|
||||
md5sum: 958e6bead4103d72026f80153b6b5150
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- samtools/sort
|
||||
files:
|
||||
- path: output/samtools/test.bam
|
||||
md5sum: 3997667dee6b45d682865c6bf82d0378
|
||||
md5sum: bdc2d9e3f579f84df1e242207b627f89
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- samtools/stats
|
||||
files:
|
||||
- path: ./output/samtools/test.paired_end.sorted.bam.stats
|
||||
md5sum: 95f7edae5d02c10c4004d9ab1d7d8ef3
|
||||
md5sum: a7f36cf11fd3bf97e0a0ae29c0627296
|
||||
|
|
|
|||
|
|
@ -4,11 +4,11 @@
|
|||
- spades
|
||||
files:
|
||||
- path: output/spades/test.assembly.gfa
|
||||
md5sum: b2616d2beba83ab7d361b54778d1e759
|
||||
md5sum: a995d1d413031534180d2b3b715fa921
|
||||
- path: output/spades/test.contigs.fa
|
||||
md5sum: 2690fefde046bc904e90df09a065257a
|
||||
md5sum: 65ba6a517c152dbe219bf4b5b92bdad7
|
||||
- path: output/spades/test.scaffolds.fa
|
||||
md5sum: 2690fefde046bc904e90df09a065257a
|
||||
md5sum: 65ba6a517c152dbe219bf4b5b92bdad7
|
||||
- path: output/spades/test.spades.log
|
||||
|
||||
- name: spades paired end
|
||||
|
|
@ -17,7 +17,7 @@
|
|||
- spades
|
||||
files:
|
||||
- path: output/spades/test.assembly.gfa
|
||||
md5sum: faf76135ee390606b899c0197dc38e04
|
||||
md5sum: bb053ef4e9250829c980ca17fbdbe3e9
|
||||
- path: output/spades/test.contigs.fa
|
||||
md5sum: 6148e25b33890c80f176f90f2dd88989
|
||||
md5sum: 4476d409da70d9f7fc2aa8f25bbaf7fd
|
||||
- path: output/spades/test.spades.log
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- tabix/bgzip
|
||||
files:
|
||||
- path: ./output/tabix/test.vcf.gz
|
||||
md5sum: 0f1c94af3aa3e7e203d9e034ef6f8f4d
|
||||
md5sum: fc178eb342a91dc0d1d568601ad8f8e2
|
||||
|
|
|
|||
|
|
@ -5,6 +5,6 @@
|
|||
- tabix/bgziptabix
|
||||
files:
|
||||
- path: ./output/tabix/test.gz
|
||||
md5sum: 0f1c94af3aa3e7e203d9e034ef6f8f4d
|
||||
md5sum: fc178eb342a91dc0d1d568601ad8f8e2
|
||||
- path: ./output/tabix/test.gz.tbi
|
||||
md5sum: bbec39fd53cf2834909d52094980d094
|
||||
md5sum: 36e11bf96ed0af4a92caa91a68612d64
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
- tabix/tabix
|
||||
files:
|
||||
- path: ./output/tabix/test.bed.gz.tbi
|
||||
md5sum: 115922d881d24879b15d20c3734495ac
|
||||
md5sum: 5b40851ab6b8ccf7946313c86481c0df
|
||||
- name: tabix tabix gff
|
||||
command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_gff -c tests/config/nextflow.config
|
||||
tags:
|
||||
|
|
@ -13,7 +13,7 @@
|
|||
- tabix/tabix
|
||||
files:
|
||||
- path: ./output/tabix/genome.gff3.gz.tbi
|
||||
md5sum: 4059fe4762568194cf293fc6df7b358b
|
||||
md5sum: f79a67d95a98076e04fbe0455d825926
|
||||
- name: tabix tabix vcf
|
||||
command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf -c tests/config/nextflow.config
|
||||
tags:
|
||||
|
|
@ -21,4 +21,4 @@
|
|||
- tabix/tabix
|
||||
files:
|
||||
- path: output/tabix/test.vcf.gz.tbi
|
||||
md5sum: bbec39fd53cf2834909d52094980d094
|
||||
md5sum: 36e11bf96ed0af4a92caa91a68612d64
|
||||
|
|
|
|||
Loading…
Reference in a new issue