From c5235a983d454787fa0c3247b02086969217163b Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 28 Jul 2021 09:10:44 +0100 Subject: [PATCH] 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 --- .nf-core.yml | 9 ++++ modules/allelecounter/main.nf | 6 +-- modules/bcftools/consensus/main.nf | 6 +-- modules/bcftools/filter/main.nf | 6 +-- modules/bcftools/isec/main.nf | 6 +-- modules/bcftools/merge/main.nf | 6 +-- modules/bcftools/mpileup/main.nf | 6 +-- modules/bcftools/stats/main.nf | 6 +-- modules/blast/blastn/main.nf | 6 +-- modules/blast/makeblastdb/main.nf | 6 +-- modules/bowtie2/build/main.nf | 6 +-- modules/cnvkit/main.nf | 6 +-- modules/cutadapt/main.nf | 6 +-- modules/deeptools/computematrix/main.nf | 6 +-- modules/deeptools/plotfingerprint/main.nf | 6 +-- modules/deeptools/plotheatmap/main.nf | 6 +-- modules/deeptools/plotprofile/main.nf | 6 +-- modules/gubbins/main.nf | 6 +-- modules/hisat2/build/main.nf | 6 +-- modules/hisat2/extractsplicesites/main.nf | 6 +-- modules/iqtree/main.nf | 6 +-- modules/kallistobustools/count/main.nf | 54 +++++++++---------- modules/kallistobustools/count/meta.yml | 26 +++------ modules/kallistobustools/ref/main.nf | 6 +-- modules/last/dotplot/main.nf | 6 +-- modules/last/lastal/main.nf | 6 +-- modules/last/lastdb/main.nf | 6 +-- modules/last/mafconvert/main.nf | 6 +-- modules/last/mafswap/main.nf | 6 +-- modules/last/postmask/main.nf | 6 +-- modules/last/split/main.nf | 6 +-- modules/last/train/main.nf | 6 +-- modules/metaphlan3/main.nf | 6 +-- modules/methyldackel/extract/main.nf | 6 +-- modules/methyldackel/mbias/main.nf | 6 +-- modules/minimap2/align/main.nf | 6 +-- modules/minimap2/index/main.nf | 6 +-- modules/mosdepth/main.nf | 6 +-- modules/multiqc/main.nf | 6 +-- modules/nanoplot/main.nf | 6 +-- modules/picard/collectmultiplemetrics/main.nf | 6 +-- modules/picard/collectwgsmetrics/main.nf | 6 +-- modules/picard/filtersamreads/main.nf | 6 +-- modules/picard/markduplicates/main.nf | 6 +-- modules/picard/mergesamfiles/main.nf | 6 +-- modules/picard/sortsam/main.nf | 6 +-- modules/prodigal/meta.yml | 10 +--- modules/raxmlng/main.nf | 6 +-- modules/salmon/index/main.nf | 6 +-- modules/salmon/quant/main.nf | 6 +-- modules/samtools/faidx/main.nf | 6 +-- modules/samtools/fastq/main.nf | 6 +-- modules/samtools/flagstat/main.nf | 6 +-- modules/samtools/idxstats/main.nf | 6 +-- modules/samtools/index/main.nf | 6 +-- modules/samtools/merge/main.nf | 6 +-- modules/samtools/mpileup/main.nf | 6 +-- modules/samtools/sort/main.nf | 6 +-- modules/samtools/stats/main.nf | 6 +-- modules/samtools/view/main.nf | 6 +-- modules/seqkit/split2/main.nf | 6 +-- modules/seqwish/induce/main.nf | 6 +-- modules/shovill/meta.yml | 8 ++- modules/spades/main.nf | 6 +-- modules/tabix/bgzip/main.nf | 6 +-- modules/tabix/bgziptabix/main.nf | 6 +-- modules/tabix/tabix/main.nf | 6 +-- modules/trimgalore/main.nf | 6 +-- tests/modules/bcftools/filter/test.yml | 2 +- tests/modules/bcftools/mpileup/test.yml | 6 +-- tests/modules/bcftools/stats/test.yml | 2 +- tests/modules/blast/blastn/test.yml | 4 +- tests/modules/blast/makeblastdb/test.yml | 4 +- .../deeptools/plotfingerprint/test.yml | 6 +-- tests/modules/gubbins/test.yml | 8 +-- tests/modules/hisat2/align/test.yml | 4 +- tests/modules/hisat2/build_test/test.yml | 2 +- tests/modules/kallistobustools/count/main.nf | 30 +++++------ tests/modules/kallistobustools/count/test.yml | 36 ++++++------- tests/modules/kallistobustools/ref/test.yml | 15 ------ tests/modules/last/lastal/test.yml | 4 +- tests/modules/last/lastdb/test.yml | 4 +- tests/modules/minimap2/align/test.yml | 4 +- tests/modules/picard/markduplicates/test.yml | 2 +- tests/modules/picard/mergesamfiles/test.yml | 2 +- tests/modules/salmon/index/test.yml | 2 +- tests/modules/salmon/quant/test.yml | 12 ++--- tests/modules/samtools/fastq/test.yml | 4 +- tests/modules/samtools/flagstat/test.yml | 2 +- tests/modules/samtools/mpileup/test.yml | 2 +- tests/modules/samtools/sort/test.yml | 2 +- tests/modules/samtools/stats/test.yml | 2 +- tests/modules/spades/test.yml | 10 ++-- tests/modules/tabix/bgzip/test.yml | 2 +- tests/modules/tabix/bgziptabix/test.yml | 4 +- tests/modules/tabix/tabix/test.yml | 6 +-- 96 files changed, 321 insertions(+), 347 deletions(-) create mode 100644 .nf-core.yml diff --git a/.nf-core.yml b/.nf-core.yml new file mode 100644 index 00000000..72971af8 --- /dev/null +++ b/.nf-core.yml @@ -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 diff --git a/modules/allelecounter/main.nf b/modules/allelecounter/main.nf index 8f090566..ad24b3c1 100644 --- a/modules/allelecounter/main.nf +++ b/modules/allelecounter/main.nf @@ -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: diff --git a/modules/bcftools/consensus/main.nf b/modules/bcftools/consensus/main.nf index 67321fc2..0403f050 100644 --- a/modules/bcftools/consensus/main.nf +++ b/modules/bcftools/consensus/main.nf @@ -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: diff --git a/modules/bcftools/filter/main.nf b/modules/bcftools/filter/main.nf index d7ec0d2b..fbdac0de 100644 --- a/modules/bcftools/filter/main.nf +++ b/modules/bcftools/filter/main.nf @@ -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: diff --git a/modules/bcftools/isec/main.nf b/modules/bcftools/isec/main.nf index b0bde522..28c6103e 100644 --- a/modules/bcftools/isec/main.nf +++ b/modules/bcftools/isec/main.nf @@ -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: diff --git a/modules/bcftools/merge/main.nf b/modules/bcftools/merge/main.nf index 09bc2e7d..66c52281 100644 --- a/modules/bcftools/merge/main.nf +++ b/modules/bcftools/merge/main.nf @@ -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: diff --git a/modules/bcftools/mpileup/main.nf b/modules/bcftools/mpileup/main.nf index 287a0c9d..de9b951f 100644 --- a/modules/bcftools/mpileup/main.nf +++ b/modules/bcftools/mpileup/main.nf @@ -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: diff --git a/modules/bcftools/stats/main.nf b/modules/bcftools/stats/main.nf index 84e48c05..90be5d2b 100644 --- a/modules/bcftools/stats/main.nf +++ b/modules/bcftools/stats/main.nf @@ -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: diff --git a/modules/blast/blastn/main.nf b/modules/blast/blastn/main.nf index 8d519613..87e012e2 100644 --- a/modules/blast/blastn/main.nf +++ b/modules/blast/blastn/main.nf @@ -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: diff --git a/modules/blast/makeblastdb/main.nf b/modules/blast/makeblastdb/main.nf index 3e3b74c2..c938e8f6 100644 --- a/modules/blast/makeblastdb/main.nf +++ b/modules/blast/makeblastdb/main.nf @@ -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: diff --git a/modules/bowtie2/build/main.nf b/modules/bowtie2/build/main.nf index 42ff1d20..442fed18 100644 --- a/modules/bowtie2/build/main.nf +++ b/modules/bowtie2/build/main.nf @@ -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: diff --git a/modules/cnvkit/main.nf b/modules/cnvkit/main.nf index dee6051d..4416919e 100755 --- a/modules/cnvkit/main.nf +++ b/modules/cnvkit/main.nf @@ -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: diff --git a/modules/cutadapt/main.nf b/modules/cutadapt/main.nf index c392367e..6dccc2bc 100644 --- a/modules/cutadapt/main.nf +++ b/modules/cutadapt/main.nf @@ -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: diff --git a/modules/deeptools/computematrix/main.nf b/modules/deeptools/computematrix/main.nf index bee16d3c..739e7cc1 100644 --- a/modules/deeptools/computematrix/main.nf +++ b/modules/deeptools/computematrix/main.nf @@ -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: diff --git a/modules/deeptools/plotfingerprint/main.nf b/modules/deeptools/plotfingerprint/main.nf index 42d5e6a2..56ecb688 100644 --- a/modules/deeptools/plotfingerprint/main.nf +++ b/modules/deeptools/plotfingerprint/main.nf @@ -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: diff --git a/modules/deeptools/plotheatmap/main.nf b/modules/deeptools/plotheatmap/main.nf index 552dc117..8e25d96f 100644 --- a/modules/deeptools/plotheatmap/main.nf +++ b/modules/deeptools/plotheatmap/main.nf @@ -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: diff --git a/modules/deeptools/plotprofile/main.nf b/modules/deeptools/plotprofile/main.nf index 59bfacd3..95f65c84 100644 --- a/modules/deeptools/plotprofile/main.nf +++ b/modules/deeptools/plotprofile/main.nf @@ -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: diff --git a/modules/gubbins/main.nf b/modules/gubbins/main.nf index 9129d14b..7f0041c8 100644 --- a/modules/gubbins/main.nf +++ b/modules/gubbins/main.nf @@ -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: diff --git a/modules/hisat2/build/main.nf b/modules/hisat2/build/main.nf index ce8bfb26..3e74b1d4 100644 --- a/modules/hisat2/build/main.nf +++ b/modules/hisat2/build/main.nf @@ -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: diff --git a/modules/hisat2/extractsplicesites/main.nf b/modules/hisat2/extractsplicesites/main.nf index 57f4dedb..d97fdb89 100644 --- a/modules/hisat2/extractsplicesites/main.nf +++ b/modules/hisat2/extractsplicesites/main.nf @@ -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: diff --git a/modules/iqtree/main.nf b/modules/iqtree/main.nf index 1eeb3a2a..3bd0f3b1 100644 --- a/modules/iqtree/main.nf +++ b/modules/iqtree/main.nf @@ -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: diff --git a/modules/kallistobustools/count/main.nf b/modules/kallistobustools/count/main.nf index 5b7416ea..86172fc3 100644 --- a/modules/kallistobustools/count/main.nf +++ b/modules/kallistobustools/count/main.nf @@ -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 """ diff --git a/modules/kallistobustools/count/meta.yml b/modules/kallistobustools/count/meta.yml index 9e6fa720..688dfdef 100644 --- a/modules/kallistobustools/count/meta.yml +++ b/modules/kallistobustools/count/meta.yml @@ -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 diff --git a/modules/kallistobustools/ref/main.nf b/modules/kallistobustools/ref/main.nf index 427251cc..ffcd643e 100644 --- a/modules/kallistobustools/ref/main.nf +++ b/modules/kallistobustools/ref/main.nf @@ -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: diff --git a/modules/last/dotplot/main.nf b/modules/last/dotplot/main.nf index 4771aa4c..3644a18e 100644 --- a/modules/last/dotplot/main.nf +++ b/modules/last/dotplot/main.nf @@ -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: diff --git a/modules/last/lastal/main.nf b/modules/last/lastal/main.nf index 4d1cb9c7..e42653cc 100644 --- a/modules/last/lastal/main.nf +++ b/modules/last/lastal/main.nf @@ -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: diff --git a/modules/last/lastdb/main.nf b/modules/last/lastdb/main.nf index ca376f67..a8cd4921 100644 --- a/modules/last/lastdb/main.nf +++ b/modules/last/lastdb/main.nf @@ -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: diff --git a/modules/last/mafconvert/main.nf b/modules/last/mafconvert/main.nf index 89c7d818..eea53dd1 100644 --- a/modules/last/mafconvert/main.nf +++ b/modules/last/mafconvert/main.nf @@ -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: diff --git a/modules/last/mafswap/main.nf b/modules/last/mafswap/main.nf index e0a697f4..03292c81 100644 --- a/modules/last/mafswap/main.nf +++ b/modules/last/mafswap/main.nf @@ -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: diff --git a/modules/last/postmask/main.nf b/modules/last/postmask/main.nf index 72584b3e..677b23f6 100644 --- a/modules/last/postmask/main.nf +++ b/modules/last/postmask/main.nf @@ -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: diff --git a/modules/last/split/main.nf b/modules/last/split/main.nf index 021b1bbf..a6fe1dda 100644 --- a/modules/last/split/main.nf +++ b/modules/last/split/main.nf @@ -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: diff --git a/modules/last/train/main.nf b/modules/last/train/main.nf index d6fd4007..cc1fa544 100644 --- a/modules/last/train/main.nf +++ b/modules/last/train/main.nf @@ -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: diff --git a/modules/metaphlan3/main.nf b/modules/metaphlan3/main.nf index 83bb9883..6c75c2a0 100644 --- a/modules/metaphlan3/main.nf +++ b/modules/metaphlan3/main.nf @@ -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: diff --git a/modules/methyldackel/extract/main.nf b/modules/methyldackel/extract/main.nf index d0a0b58d..4c7da3f4 100644 --- a/modules/methyldackel/extract/main.nf +++ b/modules/methyldackel/extract/main.nf @@ -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: diff --git a/modules/methyldackel/mbias/main.nf b/modules/methyldackel/mbias/main.nf index dcff677e..7c18197f 100644 --- a/modules/methyldackel/mbias/main.nf +++ b/modules/methyldackel/mbias/main.nf @@ -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: diff --git a/modules/minimap2/align/main.nf b/modules/minimap2/align/main.nf index 71b745a3..ec5f6a07 100644 --- a/modules/minimap2/align/main.nf +++ b/modules/minimap2/align/main.nf @@ -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: diff --git a/modules/minimap2/index/main.nf b/modules/minimap2/index/main.nf index ee0c1b36..e143bd62 100644 --- a/modules/minimap2/index/main.nf +++ b/modules/minimap2/index/main.nf @@ -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: diff --git a/modules/mosdepth/main.nf b/modules/mosdepth/main.nf index 618efd79..6beea37a 100644 --- a/modules/mosdepth/main.nf +++ b/modules/mosdepth/main.nf @@ -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: diff --git a/modules/multiqc/main.nf b/modules/multiqc/main.nf index da780800..8b6d6f0c 100644 --- a/modules/multiqc/main.nf +++ b/modules/multiqc/main.nf @@ -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: diff --git a/modules/nanoplot/main.nf b/modules/nanoplot/main.nf index af080dc8..f5fffe13 100644 --- a/modules/nanoplot/main.nf +++ b/modules/nanoplot/main.nf @@ -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: diff --git a/modules/picard/collectmultiplemetrics/main.nf b/modules/picard/collectmultiplemetrics/main.nf index c0059a40..81547e84 100644 --- a/modules/picard/collectmultiplemetrics/main.nf +++ b/modules/picard/collectmultiplemetrics/main.nf @@ -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: diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf index f1c69d28..2f01354c 100644 --- a/modules/picard/collectwgsmetrics/main.nf +++ b/modules/picard/collectwgsmetrics/main.nf @@ -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: diff --git a/modules/picard/filtersamreads/main.nf b/modules/picard/filtersamreads/main.nf index c22bbaa3..22b8c5a8 100644 --- a/modules/picard/filtersamreads/main.nf +++ b/modules/picard/filtersamreads/main.nf @@ -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: diff --git a/modules/picard/markduplicates/main.nf b/modules/picard/markduplicates/main.nf index d7647414..d20014bf 100644 --- a/modules/picard/markduplicates/main.nf +++ b/modules/picard/markduplicates/main.nf @@ -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: diff --git a/modules/picard/mergesamfiles/main.nf b/modules/picard/mergesamfiles/main.nf index abbfae8f..9fd28af6 100644 --- a/modules/picard/mergesamfiles/main.nf +++ b/modules/picard/mergesamfiles/main.nf @@ -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: diff --git a/modules/picard/sortsam/main.nf b/modules/picard/sortsam/main.nf index 2af28496..bb815c8f 100644 --- a/modules/picard/sortsam/main.nf +++ b/modules/picard/sortsam/main.nf @@ -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: diff --git a/modules/prodigal/meta.yml b/modules/prodigal/meta.yml index 10e0a3eb..f48fe96d 100644 --- a/modules/prodigal/meta.yml +++ b/modules/prodigal/meta.yml @@ -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 diff --git a/modules/raxmlng/main.nf b/modules/raxmlng/main.nf index 02c01927..9f8597b5 100644 --- a/modules/raxmlng/main.nf +++ b/modules/raxmlng/main.nf @@ -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: diff --git a/modules/salmon/index/main.nf b/modules/salmon/index/main.nf index 17d5bc06..e72ff121 100644 --- a/modules/salmon/index/main.nf +++ b/modules/salmon/index/main.nf @@ -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: diff --git a/modules/salmon/quant/main.nf b/modules/salmon/quant/main.nf index 093137de..1b9b5803 100644 --- a/modules/salmon/quant/main.nf +++ b/modules/salmon/quant/main.nf @@ -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: diff --git a/modules/samtools/faidx/main.nf b/modules/samtools/faidx/main.nf index 6c023f1c..a89ff2bb 100644 --- a/modules/samtools/faidx/main.nf +++ b/modules/samtools/faidx/main.nf @@ -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: diff --git a/modules/samtools/fastq/main.nf b/modules/samtools/fastq/main.nf index 48b3a43f..6bedbb4e 100644 --- a/modules/samtools/fastq/main.nf +++ b/modules/samtools/fastq/main.nf @@ -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: diff --git a/modules/samtools/flagstat/main.nf b/modules/samtools/flagstat/main.nf index a66ea56d..d4852c66 100644 --- a/modules/samtools/flagstat/main.nf +++ b/modules/samtools/flagstat/main.nf @@ -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: diff --git a/modules/samtools/idxstats/main.nf b/modules/samtools/idxstats/main.nf index ff3cd9a6..14a07cfb 100644 --- a/modules/samtools/idxstats/main.nf +++ b/modules/samtools/idxstats/main.nf @@ -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: diff --git a/modules/samtools/index/main.nf b/modules/samtools/index/main.nf index 778e9384..e1966fb3 100644 --- a/modules/samtools/index/main.nf +++ b/modules/samtools/index/main.nf @@ -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: diff --git a/modules/samtools/merge/main.nf b/modules/samtools/merge/main.nf index 23b31e2f..0182b9fd 100644 --- a/modules/samtools/merge/main.nf +++ b/modules/samtools/merge/main.nf @@ -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: diff --git a/modules/samtools/mpileup/main.nf b/modules/samtools/mpileup/main.nf index 8f2cebd1..f736e9c7 100644 --- a/modules/samtools/mpileup/main.nf +++ b/modules/samtools/mpileup/main.nf @@ -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: diff --git a/modules/samtools/sort/main.nf b/modules/samtools/sort/main.nf index 240e8e9f..0a6b7048 100644 --- a/modules/samtools/sort/main.nf +++ b/modules/samtools/sort/main.nf @@ -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: diff --git a/modules/samtools/stats/main.nf b/modules/samtools/stats/main.nf index 6bb0a4c7..8c72d725 100644 --- a/modules/samtools/stats/main.nf +++ b/modules/samtools/stats/main.nf @@ -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: diff --git a/modules/samtools/view/main.nf b/modules/samtools/view/main.nf index ec6c747f..2ca57032 100644 --- a/modules/samtools/view/main.nf +++ b/modules/samtools/view/main.nf @@ -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: diff --git a/modules/seqkit/split2/main.nf b/modules/seqkit/split2/main.nf index 4c516c93..5eeb0ad0 100644 --- a/modules/seqkit/split2/main.nf +++ b/modules/seqkit/split2/main.nf @@ -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: diff --git a/modules/seqwish/induce/main.nf b/modules/seqwish/induce/main.nf index 64ecd595..defd86e2 100644 --- a/modules/seqwish/induce/main.nf +++ b/modules/seqwish/induce/main.nf @@ -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: diff --git a/modules/shovill/meta.yml b/modules/shovill/meta.yml index 0a8661b1..b8f24e34 100644 --- a/modules/shovill/meta.yml +++ b/modules/shovill/meta.yml @@ -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: diff --git a/modules/spades/main.nf b/modules/spades/main.nf index c6208053..e78500f2 100644 --- a/modules/spades/main.nf +++ b/modules/spades/main.nf @@ -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: diff --git a/modules/tabix/bgzip/main.nf b/modules/tabix/bgzip/main.nf index 56a351db..e9d2e96e 100644 --- a/modules/tabix/bgzip/main.nf +++ b/modules/tabix/bgzip/main.nf @@ -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: diff --git a/modules/tabix/bgziptabix/main.nf b/modules/tabix/bgziptabix/main.nf index 866a8bf8..6cc3322f 100644 --- a/modules/tabix/bgziptabix/main.nf +++ b/modules/tabix/bgziptabix/main.nf @@ -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: diff --git a/modules/tabix/tabix/main.nf b/modules/tabix/tabix/main.nf index da23f535..df1e84ee 100644 --- a/modules/tabix/tabix/main.nf +++ b/modules/tabix/tabix/main.nf @@ -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: diff --git a/modules/trimgalore/main.nf b/modules/trimgalore/main.nf index 44b36e71..3c16d66f 100644 --- a/modules/trimgalore/main.nf +++ b/modules/trimgalore/main.nf @@ -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: diff --git a/tests/modules/bcftools/filter/test.yml b/tests/modules/bcftools/filter/test.yml index a998f441..0f8e48eb 100644 --- a/tests/modules/bcftools/filter/test.yml +++ b/tests/modules/bcftools/filter/test.yml @@ -5,4 +5,4 @@ - bcftools files: - path: output/bcftools/test.vcf.gz - md5sum: 9d491cfa84067450342ba8e66c75e5b8 + md5sum: fc178eb342a91dc0d1d568601ad8f8e2 diff --git a/tests/modules/bcftools/mpileup/test.yml b/tests/modules/bcftools/mpileup/test.yml index c0c8d6a6..71877e29 100644 --- a/tests/modules/bcftools/mpileup/test.yml +++ b/tests/modules/bcftools/mpileup/test.yml @@ -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 diff --git a/tests/modules/bcftools/stats/test.yml b/tests/modules/bcftools/stats/test.yml index f863bfca..cd25fe66 100644 --- a/tests/modules/bcftools/stats/test.yml +++ b/tests/modules/bcftools/stats/test.yml @@ -5,4 +5,4 @@ - bcftools/stats files: - path: output/bcftools/test.bcftools_stats.txt - md5sum: c4c5938add12a20050eec3782c8ad623 + md5sum: d3543531396cf7012f13ebdce639cbc8 diff --git a/tests/modules/blast/blastn/test.yml b/tests/modules/blast/blastn/test.yml index ebc03e45..98f76921 100644 --- a/tests/modules/blast/blastn/test.yml +++ b/tests/modules/blast/blastn/test.yml @@ -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 diff --git a/tests/modules/blast/makeblastdb/test.yml b/tests/modules/blast/makeblastdb/test.yml index c060ba59..7df17968 100644 --- a/tests/modules/blast/makeblastdb/test.yml +++ b/tests/modules/blast/makeblastdb/test.yml @@ -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 diff --git a/tests/modules/deeptools/plotfingerprint/test.yml b/tests/modules/deeptools/plotfingerprint/test.yml index bb96fbe2..b7803a6e 100644 --- a/tests/modules/deeptools/plotfingerprint/test.yml +++ b/tests/modules/deeptools/plotfingerprint/test.yml @@ -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 diff --git a/tests/modules/gubbins/test.yml b/tests/modules/gubbins/test.yml index 31e426b1..7bc0216b 100644 --- a/tests/modules/gubbins/test.yml +++ b/tests/modules/gubbins/test.yml @@ -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 diff --git a/tests/modules/hisat2/align/test.yml b/tests/modules/hisat2/align/test.yml index 9a1fb271..1c6c8ac2 100644 --- a/tests/modules/hisat2/align/test.yml +++ b/tests/modules/hisat2/align/test.yml @@ -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 diff --git a/tests/modules/hisat2/build_test/test.yml b/tests/modules/hisat2/build_test/test.yml index 2a8fe324..a8bb2390 100644 --- a/tests/modules/hisat2/build_test/test.yml +++ b/tests/modules/hisat2/build_test/test.yml @@ -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 diff --git a/tests/modules/kallistobustools/count/main.nf b/tests/modules/kallistobustools/count/main.nf index 051195af..4400976a 100644 --- a/tests/modules/kallistobustools/count/main.nf +++ b/tests/modules/kallistobustools/count/main.nf @@ -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 ) } diff --git a/tests/modules/kallistobustools/count/test.yml b/tests/modules/kallistobustools/count/test.yml index 8ff9a66f..766d5b57 100644 --- a/tests/modules/kallistobustools/count/test.yml +++ b/tests/modules/kallistobustools/count/test.yml @@ -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 diff --git a/tests/modules/kallistobustools/ref/test.yml b/tests/modules/kallistobustools/ref/test.yml index 1821533a..54954085 100644 --- a/tests/modules/kallistobustools/ref/test.yml +++ b/tests/modules/kallistobustools/ref/test.yml @@ -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 diff --git a/tests/modules/last/lastal/test.yml b/tests/modules/last/lastal/test.yml index c6966a5f..48b0d223 100644 --- a/tests/modules/last/lastal/test.yml +++ b/tests/modules/last/lastal/test.yml @@ -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 diff --git a/tests/modules/last/lastdb/test.yml b/tests/modules/last/lastdb/test.yml index fed274eb..c69ecfac 100644 --- a/tests/modules/last/lastdb/test.yml +++ b/tests/modules/last/lastdb/test.yml @@ -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 diff --git a/tests/modules/minimap2/align/test.yml b/tests/modules/minimap2/align/test.yml index 484fa9f7..f9b762bb 100644 --- a/tests/modules/minimap2/align/test.yml +++ b/tests/modules/minimap2/align/test.yml @@ -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 diff --git a/tests/modules/picard/markduplicates/test.yml b/tests/modules/picard/markduplicates/test.yml index db3cf253..24f468ce 100644 --- a/tests/modules/picard/markduplicates/test.yml +++ b/tests/modules/picard/markduplicates/test.yml @@ -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 diff --git a/tests/modules/picard/mergesamfiles/test.yml b/tests/modules/picard/mergesamfiles/test.yml index be82034f..114c1f01 100644 --- a/tests/modules/picard/mergesamfiles/test.yml +++ b/tests/modules/picard/mergesamfiles/test.yml @@ -5,4 +5,4 @@ - picard/mergesamfiles files: - path: ./output/picard/test.bam - md5sum: b8bd6c22f36c6ebc91bca98bd637a2eb + md5sum: 82bb91735aff82eae4f0b631114e9e15 diff --git a/tests/modules/salmon/index/test.yml b/tests/modules/salmon/index/test.yml index 722cd24f..156bc5ca 100644 --- a/tests/modules/salmon/index/test.yml +++ b/tests/modules/salmon/index/test.yml @@ -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 diff --git a/tests/modules/salmon/quant/test.yml b/tests/modules/salmon/quant/test.yml index 5a1ebdd8..d7ed0d0f 100644 --- a/tests/modules/salmon/quant/test.yml +++ b/tests/modules/salmon/quant/test.yml @@ -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 diff --git a/tests/modules/samtools/fastq/test.yml b/tests/modules/samtools/fastq/test.yml index 3fdc0ef6..bfcf5c92 100644 --- a/tests/modules/samtools/fastq/test.yml +++ b/tests/modules/samtools/fastq/test.yml @@ -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 diff --git a/tests/modules/samtools/flagstat/test.yml b/tests/modules/samtools/flagstat/test.yml index 18671e25..0da6c2f4 100644 --- a/tests/modules/samtools/flagstat/test.yml +++ b/tests/modules/samtools/flagstat/test.yml @@ -5,4 +5,4 @@ - samtools/flagstat files: - path: ./output/samtools/test.paired_end.sorted.bam.flagstat - md5sum: 6d7934c303b15ce473f64d502b79984e + md5sum: 4f7ffd1e6a5e85524d443209ac97d783 diff --git a/tests/modules/samtools/mpileup/test.yml b/tests/modules/samtools/mpileup/test.yml index 31d35c0f..25c39d63 100644 --- a/tests/modules/samtools/mpileup/test.yml +++ b/tests/modules/samtools/mpileup/test.yml @@ -5,4 +5,4 @@ - samtools/mpileup files: - path: ./output/samtools/test.mpileup - md5sum: 3608af83ffe3efbb1337f0ffb205337d + md5sum: 958e6bead4103d72026f80153b6b5150 diff --git a/tests/modules/samtools/sort/test.yml b/tests/modules/samtools/sort/test.yml index 2ce00247..477574fe 100644 --- a/tests/modules/samtools/sort/test.yml +++ b/tests/modules/samtools/sort/test.yml @@ -5,4 +5,4 @@ - samtools/sort files: - path: output/samtools/test.bam - md5sum: 3997667dee6b45d682865c6bf82d0378 + md5sum: bdc2d9e3f579f84df1e242207b627f89 diff --git a/tests/modules/samtools/stats/test.yml b/tests/modules/samtools/stats/test.yml index 32854c05..cf44b846 100644 --- a/tests/modules/samtools/stats/test.yml +++ b/tests/modules/samtools/stats/test.yml @@ -5,4 +5,4 @@ - samtools/stats files: - path: ./output/samtools/test.paired_end.sorted.bam.stats - md5sum: 95f7edae5d02c10c4004d9ab1d7d8ef3 + md5sum: a7f36cf11fd3bf97e0a0ae29c0627296 diff --git a/tests/modules/spades/test.yml b/tests/modules/spades/test.yml index eeff24cd..35beb1a7 100644 --- a/tests/modules/spades/test.yml +++ b/tests/modules/spades/test.yml @@ -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 diff --git a/tests/modules/tabix/bgzip/test.yml b/tests/modules/tabix/bgzip/test.yml index e254daed..58412979 100644 --- a/tests/modules/tabix/bgzip/test.yml +++ b/tests/modules/tabix/bgzip/test.yml @@ -5,4 +5,4 @@ - tabix/bgzip files: - path: ./output/tabix/test.vcf.gz - md5sum: 0f1c94af3aa3e7e203d9e034ef6f8f4d + md5sum: fc178eb342a91dc0d1d568601ad8f8e2 diff --git a/tests/modules/tabix/bgziptabix/test.yml b/tests/modules/tabix/bgziptabix/test.yml index c0b9c247..31048109 100644 --- a/tests/modules/tabix/bgziptabix/test.yml +++ b/tests/modules/tabix/bgziptabix/test.yml @@ -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 diff --git a/tests/modules/tabix/tabix/test.yml b/tests/modules/tabix/tabix/test.yml index 41c4a940..646215c8 100644 --- a/tests/modules/tabix/tabix/test.yml +++ b/tests/modules/tabix/tabix/test.yml @@ -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