From 8a442585482167c3d7cd5a724d0d705182d1176c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Patrick=20H=C3=BCther?= Date: Fri, 19 Mar 2021 13:16:50 +0100 Subject: [PATCH] remove params section from meta.yml (#282) --- software/bandage/image/meta.yml | 21 ---------- software/bcftools/consensus/meta.yml | 21 ---------- software/bcftools/filter/meta.yml | 21 ---------- software/bcftools/isec/meta.yml | 21 ---------- software/bcftools/merge/meta.yml | 21 ---------- software/bcftools/mpileup/meta.yml | 21 ---------- software/bcftools/stats/meta.yml | 21 ---------- software/bedtools/complement/meta.yml | 21 ---------- software/bedtools/genomecov/meta.yml | 21 ---------- software/bedtools/getfasta/meta.yml | 21 ---------- software/bedtools/intersect/meta.yml | 21 ---------- software/bedtools/maskfasta/meta.yml | 21 ---------- software/bedtools/merge/meta.yml | 21 ---------- software/bedtools/slop/meta.yml | 21 ---------- software/bedtools/sort/meta.yml | 21 ---------- software/bismark/deduplicate/meta.yml | 21 ---------- software/bismark/genome_preparation/meta.yml | 21 ---------- software/blast/blastn/meta.yml | 21 ---------- software/blast/makeblastdb/meta.yml | 21 ---------- software/bowtie/align/meta.yml | 24 ----------- software/bowtie/build/meta.yml | 21 ---------- software/bowtie2/align/meta.yml | 24 ----------- software/bowtie2/build/meta.yml | 21 ---------- software/bwa/index/meta.yml | 21 ---------- software/bwa/mem/meta.yml | 21 ---------- software/bwamem2/index/meta.yml | 21 ---------- software/bwamem2/mem/meta.yml | 21 ---------- software/bwameth/align/meta.yml | 21 ---------- software/bwameth/index/meta.yml | 21 ---------- software/cat/fastq/meta.yml | 21 ---------- software/cutadapt/meta.yml | 21 ---------- software/dsh/filterbed/meta.yml | 21 ---------- software/dsh/splitbed/meta.yml | 21 ---------- software/fastp/meta.yml | 22 ---------- software/fastqc/meta.yml | 21 ---------- software/gatk4/bedtointervallist/meta.yml | 21 ---------- .../gatk4/createsequencedictionary/meta.yml | 21 ---------- software/gatk4/mergebamalignment/meta.yml | 21 ---------- software/gatk4/mergevcfs/meta.yml | 21 ---------- software/gatk4/revertsam/meta.yml | 21 ---------- software/gatk4/samtofastq/meta.yml | 21 ---------- software/gatk4/splitncigarreads/meta.yml | 21 ---------- software/gatk4/variantfiltration/meta.yml | 21 ---------- software/gunzip/meta.yml | 21 ---------- software/ivar/consensus/meta.yml | 21 ---------- software/ivar/trim/meta.yml | 21 ---------- software/ivar/variants/meta.yml | 21 ---------- software/methyldackel/extract/meta.yml | 21 ---------- software/methyldackel/mbias/meta.yml | 21 ---------- software/minia/meta.yml | 21 ---------- software/minimap2/align/meta.yml | 21 ---------- software/mosdepth/meta.yml | 21 ---------- software/multiqc/meta.yml | 21 ---------- software/pangolin/meta.yml | 21 ---------- .../picard/collectmultiplemetrics/meta.yml | 21 ---------- software/picard/markduplicates/meta.yml | 21 ---------- software/picard/mergesamfiles/meta.yml | 21 ---------- software/qualimap/bamqc/meta.yml | 21 ---------- software/quast/meta.yml | 22 ---------- software/salmon/index/meta.yml | 22 ---------- software/salmon/quant/meta.yml | 22 ---------- software/samtools/faidx/meta.yml | 21 ---------- software/samtools/flagstat/meta.yml | 21 ---------- software/samtools/idxstats/meta.yml | 21 ---------- software/samtools/index/meta.yml | 21 ---------- software/samtools/mpileup/meta.yml | 21 ---------- software/samtools/sort/meta.yml | 21 ---------- software/samtools/stats/meta.yml | 21 ---------- software/samtools/view/meta.yml | 21 ---------- software/seacr/callpeak/meta.yml | 21 ---------- software/seqkit/split2/meta.yml | 21 ---------- software/seqwish/induce/meta.yml | 21 ---------- software/star/align/meta.yml | 22 ---------- software/star/genomegenerate/meta.yml | 22 ---------- software/tabix/bgzip/meta.yml | 21 ---------- software/tabix/tabix/meta.yml | 21 ---------- software/tiddit/sv/meta.yml | 21 ---------- software/trimgalore/meta.yml | 41 ------------------- software/untar/meta.yml | 21 ---------- 79 files changed, 1691 deletions(-) diff --git a/software/bandage/image/meta.yml b/software/bandage/image/meta.yml index 85de09a2..26c23a07 100644 --- a/software/bandage/image/meta.yml +++ b/software/bandage/image/meta.yml @@ -11,27 +11,6 @@ tools: Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily homepage: https://github.com/rrwick/Bandage documentation: https://github.com/rrwick/Bandage -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/bcftools/consensus/meta.yml b/software/bcftools/consensus/meta.yml index 6cb15f11..ef14479d 100644 --- a/software/bcftools/consensus/meta.yml +++ b/software/bcftools/consensus/meta.yml @@ -11,27 +11,6 @@ tools: homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/bcftools/filter/meta.yml b/software/bcftools/filter/meta.yml index 68fe9d47..fe9a57e6 100644 --- a/software/bcftools/filter/meta.yml +++ b/software/bcftools/filter/meta.yml @@ -11,27 +11,6 @@ tools: homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/bcftools/isec/meta.yml b/software/bcftools/isec/meta.yml index 415a3546..fb8f4b4e 100644 --- a/software/bcftools/isec/meta.yml +++ b/software/bcftools/isec/meta.yml @@ -13,27 +13,6 @@ tools: homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/bcftools/merge/meta.yml b/software/bcftools/merge/meta.yml index b4a1f9cb..fad7966e 100644 --- a/software/bcftools/merge/meta.yml +++ b/software/bcftools/merge/meta.yml @@ -11,27 +11,6 @@ tools: homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/bcftools/mpileup/meta.yml b/software/bcftools/mpileup/meta.yml index c87d0619..a15aea14 100644 --- a/software/bcftools/mpileup/meta.yml +++ b/software/bcftools/mpileup/meta.yml @@ -11,27 +11,6 @@ tools: homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/bcftools/stats/meta.yml b/software/bcftools/stats/meta.yml index 75ed50f4..6b70f83a 100644 --- a/software/bcftools/stats/meta.yml +++ b/software/bcftools/stats/meta.yml @@ -12,27 +12,6 @@ tools: homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/bedtools/complement/meta.yml b/software/bedtools/complement/meta.yml index 9e0a2dd8..60d97263 100644 --- a/software/bedtools/complement/meta.yml +++ b/software/bedtools/complement/meta.yml @@ -8,27 +8,6 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/bedtools/genomecov/meta.yml b/software/bedtools/genomecov/meta.yml index b18958a7..a3254307 100644 --- a/software/bedtools/genomecov/meta.yml +++ b/software/bedtools/genomecov/meta.yml @@ -9,27 +9,6 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/bedtools/getfasta/meta.yml b/software/bedtools/getfasta/meta.yml index 692b7028..1ca63bdc 100644 --- a/software/bedtools/getfasta/meta.yml +++ b/software/bedtools/getfasta/meta.yml @@ -9,27 +9,6 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - bed: type: file diff --git a/software/bedtools/intersect/meta.yml b/software/bedtools/intersect/meta.yml index 5a72df53..eaba54f6 100644 --- a/software/bedtools/intersect/meta.yml +++ b/software/bedtools/intersect/meta.yml @@ -8,27 +8,6 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/bedtools/maskfasta/meta.yml b/software/bedtools/maskfasta/meta.yml index ef4e4096..b6e494e6 100644 --- a/software/bedtools/maskfasta/meta.yml +++ b/software/bedtools/maskfasta/meta.yml @@ -9,27 +9,6 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/bedtools/merge/meta.yml b/software/bedtools/merge/meta.yml index 1aec9234..f75bea67 100644 --- a/software/bedtools/merge/meta.yml +++ b/software/bedtools/merge/meta.yml @@ -8,27 +8,6 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/bedtools/slop/meta.yml b/software/bedtools/slop/meta.yml index 3f56b38e..3d4e2091 100644 --- a/software/bedtools/slop/meta.yml +++ b/software/bedtools/slop/meta.yml @@ -8,27 +8,6 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/bedtools/sort/meta.yml b/software/bedtools/sort/meta.yml index dde823bd..9962a4f2 100644 --- a/software/bedtools/sort/meta.yml +++ b/software/bedtools/sort/meta.yml @@ -8,27 +8,6 @@ tools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/bismark/deduplicate/meta.yml b/software/bismark/deduplicate/meta.yml index 59a99a7f..117eed49 100644 --- a/software/bismark/deduplicate/meta.yml +++ b/software/bismark/deduplicate/meta.yml @@ -19,27 +19,6 @@ tools: homepage: https://github.com/FelixKrueger/Bismark documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/bismark/genome_preparation/meta.yml b/software/bismark/genome_preparation/meta.yml index 4bd10db7..f357ffb1 100644 --- a/software/bismark/genome_preparation/meta.yml +++ b/software/bismark/genome_preparation/meta.yml @@ -19,27 +19,6 @@ tools: homepage: https://github.com/FelixKrueger/Bismark documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - fasta: type: file diff --git a/software/blast/blastn/meta.yml b/software/blast/blastn/meta.yml index 41dd872d..d04889a8 100644 --- a/software/blast/blastn/meta.yml +++ b/software/blast/blastn/meta.yml @@ -12,27 +12,6 @@ tools: homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs doi: 10.1016/S0022-2836(05)80360-2 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/blast/makeblastdb/meta.yml b/software/blast/makeblastdb/meta.yml index 0629a49a..0ea4903f 100644 --- a/software/blast/makeblastdb/meta.yml +++ b/software/blast/makeblastdb/meta.yml @@ -11,27 +11,6 @@ tools: homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs doi: 10.1016/S0022-2836(05)80360-2 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - fasta: type: file diff --git a/software/bowtie/align/meta.yml b/software/bowtie/align/meta.yml index ebadcdca..bea8b4dd 100644 --- a/software/bowtie/align/meta.yml +++ b/software/bowtie/align/meta.yml @@ -13,30 +13,6 @@ tools: homepage: http://bowtie-bio.sourceforge.net/index.shtml documentation: http://bowtie-bio.sourceforge.net/manual.shtml arxiv: arXiv:1303.3997 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. - - save_unaligned: - type: boolean - description: Save unaligned reads input: - meta: type: map diff --git a/software/bowtie/build/meta.yml b/software/bowtie/build/meta.yml index f9a8f1c9..a2da42c6 100644 --- a/software/bowtie/build/meta.yml +++ b/software/bowtie/build/meta.yml @@ -13,27 +13,6 @@ tools: homepage: http://bowtie-bio.sourceforge.net/index.shtml documentation: http://bowtie-bio.sourceforge.net/manual.shtml arxiv: arXiv:1303.3997 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - fasta: type: file diff --git a/software/bowtie2/align/meta.yml b/software/bowtie2/align/meta.yml index eb78e9f9..9d9cd004 100644 --- a/software/bowtie2/align/meta.yml +++ b/software/bowtie2/align/meta.yml @@ -13,30 +13,6 @@ tools: homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml doi: 10.1038/nmeth.1923 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. - - save_unaligned: - type: boolean - description: Save unaligned reads input: - meta: type: map diff --git a/software/bowtie2/build/meta.yml b/software/bowtie2/build/meta.yml index 959a9b09..0a4cd3de 100644 --- a/software/bowtie2/build/meta.yml +++ b/software/bowtie2/build/meta.yml @@ -14,27 +14,6 @@ tools: homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml doi: 10.1038/nmeth.1923 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - fasta: type: file diff --git a/software/bwa/index/meta.yml b/software/bwa/index/meta.yml index 0c3b8f5f..181204c3 100644 --- a/software/bwa/index/meta.yml +++ b/software/bwa/index/meta.yml @@ -13,27 +13,6 @@ tools: homepage: http://bio-bwa.sourceforge.net/ documentation: http://www.htslib.org/doc/samtools.html arxiv: arXiv:1303.3997 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - fasta: type: file diff --git a/software/bwa/mem/meta.yml b/software/bwa/mem/meta.yml index 2e44951c..693c5450 100644 --- a/software/bwa/mem/meta.yml +++ b/software/bwa/mem/meta.yml @@ -16,27 +16,6 @@ tools: homepage: http://bio-bwa.sourceforge.net/ documentation: http://www.htslib.org/doc/samtools.html arxiv: arXiv:1303.3997 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/bwamem2/index/meta.yml b/software/bwamem2/index/meta.yml index 70780902..9d717f73 100644 --- a/software/bwamem2/index/meta.yml +++ b/software/bwamem2/index/meta.yml @@ -12,27 +12,6 @@ tools: a large reference genome, such as the human genome. homepage: https://github.com/bwa-mem2/bwa-mem2 documentation: https://github.com/bwa-mem2/bwa-mem2#usage -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - fasta: type: file diff --git a/software/bwamem2/mem/meta.yml b/software/bwamem2/mem/meta.yml index 7d59b9b4..2fc7713d 100644 --- a/software/bwamem2/mem/meta.yml +++ b/software/bwamem2/mem/meta.yml @@ -16,27 +16,6 @@ tools: homepage: http://bio-bwa.sourceforge.net/ documentation: http://www.htslib.org/doc/samtools.html arxiv: arXiv:1303.3997 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/bwameth/align/meta.yml b/software/bwameth/align/meta.yml index 9d46e4cc..ac578031 100644 --- a/software/bwameth/align/meta.yml +++ b/software/bwameth/align/meta.yml @@ -19,27 +19,6 @@ tools: homepage: https://github.com/brentp/bwa-meth documentation: https://github.com/brentp/bwa-meth arxiv: arXiv:1401.1129 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/bwameth/index/meta.yml b/software/bwameth/index/meta.yml index 467a2758..79c54862 100644 --- a/software/bwameth/index/meta.yml +++ b/software/bwameth/index/meta.yml @@ -15,27 +15,6 @@ tools: homepage: https://github.com/brentp/bwa-meth documentation: https://github.com/brentp/bwa-meth arxiv: arXiv:1401.1129 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - fasta: type: file diff --git a/software/cat/fastq/meta.yml b/software/cat/fastq/meta.yml index 5807bdde..e7b8eebe 100644 --- a/software/cat/fastq/meta.yml +++ b/software/cat/fastq/meta.yml @@ -8,27 +8,6 @@ tools: description: | The cat utility reads files sequentially, writing them to the standard output. documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/cutadapt/meta.yml b/software/cutadapt/meta.yml index 3e50c750..14652343 100644 --- a/software/cutadapt/meta.yml +++ b/software/cutadapt/meta.yml @@ -11,27 +11,6 @@ tools: Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. documentation: https://cutadapt.readthedocs.io/en/stable/index.html doi: DOI:10.14806/ej.17.1.200 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/dsh/filterbed/meta.yml b/software/dsh/filterbed/meta.yml index 6790ce0e..4b3d5fb4 100644 --- a/software/dsh/filterbed/meta.yml +++ b/software/dsh/filterbed/meta.yml @@ -10,27 +10,6 @@ tools: or later. homepage: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/dsh/splitbed/meta.yml b/software/dsh/splitbed/meta.yml index b2950e01..9136efe7 100644 --- a/software/dsh/splitbed/meta.yml +++ b/software/dsh/splitbed/meta.yml @@ -10,27 +10,6 @@ tools: or later. homepage: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/fastp/meta.yml b/software/fastp/meta.yml index 2846d834..bbf2f1ca 100644 --- a/software/fastp/meta.yml +++ b/software/fastp/meta.yml @@ -10,28 +10,6 @@ tools: A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. documentation: https://github.com/OpenGene/fastp doi: https://doi.org/10.1093/bioinformatics/bty560 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. - input: - meta: type: map diff --git a/software/fastqc/meta.yml b/software/fastqc/meta.yml index 413aad8d..8eb9953d 100644 --- a/software/fastqc/meta.yml +++ b/software/fastqc/meta.yml @@ -15,27 +15,6 @@ tools: overrepresented sequences. homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/gatk4/bedtointervallist/meta.yml b/software/gatk4/bedtointervallist/meta.yml index 4ed8629e..23e98447 100644 --- a/software/gatk4/bedtointervallist/meta.yml +++ b/software/gatk4/bedtointervallist/meta.yml @@ -12,27 +12,6 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/gatk4/createsequencedictionary/meta.yml b/software/gatk4/createsequencedictionary/meta.yml index b33af6ad..d0cc5980 100644 --- a/software/gatk4/createsequencedictionary/meta.yml +++ b/software/gatk4/createsequencedictionary/meta.yml @@ -12,27 +12,6 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - fasta: type: file diff --git a/software/gatk4/mergebamalignment/meta.yml b/software/gatk4/mergebamalignment/meta.yml index c45f5a22..155b6364 100644 --- a/software/gatk4/mergebamalignment/meta.yml +++ b/software/gatk4/mergebamalignment/meta.yml @@ -12,27 +12,6 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/gatk4/mergevcfs/meta.yml b/software/gatk4/mergevcfs/meta.yml index 5d6e053d..14b28fa0 100644 --- a/software/gatk4/mergevcfs/meta.yml +++ b/software/gatk4/mergevcfs/meta.yml @@ -12,27 +12,6 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/gatk4/revertsam/meta.yml b/software/gatk4/revertsam/meta.yml index e7d176c8..258bb253 100644 --- a/software/gatk4/revertsam/meta.yml +++ b/software/gatk4/revertsam/meta.yml @@ -12,27 +12,6 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/gatk4/samtofastq/meta.yml b/software/gatk4/samtofastq/meta.yml index 8d8d2336..0601f3a7 100644 --- a/software/gatk4/samtofastq/meta.yml +++ b/software/gatk4/samtofastq/meta.yml @@ -12,27 +12,6 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/gatk4/splitncigarreads/meta.yml b/software/gatk4/splitncigarreads/meta.yml index 33610180..e433cbf6 100644 --- a/software/gatk4/splitncigarreads/meta.yml +++ b/software/gatk4/splitncigarreads/meta.yml @@ -12,27 +12,6 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/gatk4/variantfiltration/meta.yml b/software/gatk4/variantfiltration/meta.yml index c7065efc..d7f72582 100644 --- a/software/gatk4/variantfiltration/meta.yml +++ b/software/gatk4/variantfiltration/meta.yml @@ -12,27 +12,6 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/gunzip/meta.yml b/software/gunzip/meta.yml index 65ae4143..922e74e6 100644 --- a/software/gunzip/meta.yml +++ b/software/gunzip/meta.yml @@ -8,27 +8,6 @@ tools: description: | gzip is a file format and a software application used for file compression and decompression. documentation: https://www.gnu.org/software/gzip/manual/gzip.html -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - archive: type: file diff --git a/software/ivar/consensus/meta.yml b/software/ivar/consensus/meta.yml index 0180c72c..913a7660 100644 --- a/software/ivar/consensus/meta.yml +++ b/software/ivar/consensus/meta.yml @@ -10,27 +10,6 @@ tools: iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. homepage: https://github.com/andersen-lab/ivar documentation: https://andersen-lab.github.io/ivar/html/manualpage.html -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/ivar/trim/meta.yml b/software/ivar/trim/meta.yml index 9d8d39df..5791db66 100644 --- a/software/ivar/trim/meta.yml +++ b/software/ivar/trim/meta.yml @@ -10,27 +10,6 @@ tools: iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. homepage: https://github.com/andersen-lab/ivar documentation: https://andersen-lab.github.io/ivar/html/manualpage.html -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/ivar/variants/meta.yml b/software/ivar/variants/meta.yml index 6f8e828a..7a5fbbc0 100644 --- a/software/ivar/variants/meta.yml +++ b/software/ivar/variants/meta.yml @@ -10,27 +10,6 @@ tools: iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. homepage: https://github.com/andersen-lab/ivar documentation: https://andersen-lab.github.io/ivar/html/manualpage.html -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/methyldackel/extract/meta.yml b/software/methyldackel/extract/meta.yml index 801a4696..525ddebe 100644 --- a/software/methyldackel/extract/meta.yml +++ b/software/methyldackel/extract/meta.yml @@ -17,27 +17,6 @@ tools: homepage: https://github.com/brentp/bwa-meth documentation: https://github.com/brentp/bwa-meth arxiv: arXiv:1401.1129 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/methyldackel/mbias/meta.yml b/software/methyldackel/mbias/meta.yml index f72a11be..e41d0208 100644 --- a/software/methyldackel/mbias/meta.yml +++ b/software/methyldackel/mbias/meta.yml @@ -18,27 +18,6 @@ tools: homepage: https://github.com/brentp/bwa-meth documentation: https://github.com/brentp/bwa-meth arxiv: arXiv:1401.1129 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/minia/meta.yml b/software/minia/meta.yml index 17f0eb7f..d3a76be8 100644 --- a/software/minia/meta.yml +++ b/software/minia/meta.yml @@ -9,27 +9,6 @@ tools: a human genome on a desktop computer in a day. The output of Minia is a set of contigs. homepage: https://github.com/GATB/minia documentation: https://github.com/GATB/minia -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/minimap2/align/meta.yml b/software/minimap2/align/meta.yml index 64c9dc3a..3c741b16 100644 --- a/software/minimap2/align/meta.yml +++ b/software/minimap2/align/meta.yml @@ -13,27 +13,6 @@ tools: A versatile pairwise aligner for genomic and spliced nucleotide sequences. homepage: https://github.com/lh3/minimap2 documentation: https://github.com/lh3/minimap2#uguide -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/mosdepth/meta.yml b/software/mosdepth/meta.yml index 7a822894..d96e474f 100644 --- a/software/mosdepth/meta.yml +++ b/software/mosdepth/meta.yml @@ -11,27 +11,6 @@ tools: Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing. documentation: https://github.com/brentp/mosdepth doi: 10.1093/bioinformatics/btx699 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/multiqc/meta.yml b/software/multiqc/meta.yml index 02f4b415..532a8bb1 100644 --- a/software/multiqc/meta.yml +++ b/software/multiqc/meta.yml @@ -11,27 +11,6 @@ tools: It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - multiqc_files: type: file diff --git a/software/pangolin/meta.yml b/software/pangolin/meta.yml index 82e157d9..2b2eb952 100644 --- a/software/pangolin/meta.yml +++ b/software/pangolin/meta.yml @@ -10,27 +10,6 @@ tools: Phylogenetic Assignment of Named Global Outbreak LINeages homepage: https://github.com/cov-lineages/pangolin#pangolearn-description manual: https://github.com/cov-lineages/pangolin#pangolearn-description -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/picard/collectmultiplemetrics/meta.yml b/software/picard/collectmultiplemetrics/meta.yml index acdbdfec..34006093 100644 --- a/software/picard/collectmultiplemetrics/meta.yml +++ b/software/picard/collectmultiplemetrics/meta.yml @@ -14,27 +14,6 @@ tools: data and formats such as SAM/BAM/CRAM and VCF. homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/picard/markduplicates/meta.yml b/software/picard/markduplicates/meta.yml index d9d8619a..6420ce9a 100644 --- a/software/picard/markduplicates/meta.yml +++ b/software/picard/markduplicates/meta.yml @@ -14,27 +14,6 @@ tools: data and formats such as SAM/BAM/CRAM and VCF. homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/picard/mergesamfiles/meta.yml b/software/picard/mergesamfiles/meta.yml index 090432b7..4ea9fd17 100644 --- a/software/picard/mergesamfiles/meta.yml +++ b/software/picard/mergesamfiles/meta.yml @@ -12,27 +12,6 @@ tools: data and formats such as SAM/BAM/CRAM and VCF. homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/qualimap/bamqc/meta.yml b/software/qualimap/bamqc/meta.yml index 61f4bc8b..3c608f31 100644 --- a/software/qualimap/bamqc/meta.yml +++ b/software/qualimap/bamqc/meta.yml @@ -14,27 +14,6 @@ tools: homepage: http://qualimap.bioinfo.cipf.es/ documentation: http://qualimap.conesalab.org/doc_html/index.html doi: 10.1093/bioinformatics/bts503 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/quast/meta.yml b/software/quast/meta.yml index dde96c97..cc79486e 100644 --- a/software/quast/meta.yml +++ b/software/quast/meta.yml @@ -10,28 +10,6 @@ tools: QUAST calculates quality metrics for genome assemblies homepage: http://bioinf.spbau.ru/quast doi: -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. - input: - consensus: type: file diff --git a/software/salmon/index/meta.yml b/software/salmon/index/meta.yml index 8d1d9292..652e2a77 100644 --- a/software/salmon/index/meta.yml +++ b/software/salmon/index/meta.yml @@ -12,28 +12,6 @@ tools: homepage: https://salmon.readthedocs.io/en/latest/salmon.html manual: https://salmon.readthedocs.io/en/latest/salmon.html doi: 10.1038/nmeth.4197 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. - input: - genome_fasta: type: file diff --git a/software/salmon/quant/meta.yml b/software/salmon/quant/meta.yml index 88db9c74..fa39aaf9 100644 --- a/software/salmon/quant/meta.yml +++ b/software/salmon/quant/meta.yml @@ -12,28 +12,6 @@ tools: homepage: https://salmon.readthedocs.io/en/latest/salmon.html manual: https://salmon.readthedocs.io/en/latest/salmon.html doi: 10.1038/nmeth.4197 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. - input: - meta: type: map diff --git a/software/samtools/faidx/meta.yml b/software/samtools/faidx/meta.yml index 2141e9b3..f92234d0 100644 --- a/software/samtools/faidx/meta.yml +++ b/software/samtools/faidx/meta.yml @@ -12,27 +12,6 @@ tools: homepage: http://www.htslib.org/ documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - fasta: type: file diff --git a/software/samtools/flagstat/meta.yml b/software/samtools/flagstat/meta.yml index a140c795..8414bf54 100644 --- a/software/samtools/flagstat/meta.yml +++ b/software/samtools/flagstat/meta.yml @@ -16,27 +16,6 @@ tools: homepage: http://www.htslib.org/ documentation: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/samtools/idxstats/meta.yml b/software/samtools/idxstats/meta.yml index 6ff30433..530d0772 100644 --- a/software/samtools/idxstats/meta.yml +++ b/software/samtools/idxstats/meta.yml @@ -17,27 +17,6 @@ tools: homepage: http://www.htslib.org/ documentation: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/samtools/index/meta.yml b/software/samtools/index/meta.yml index 089a83be..03936e59 100644 --- a/software/samtools/index/meta.yml +++ b/software/samtools/index/meta.yml @@ -14,27 +14,6 @@ tools: homepage: http://www.htslib.org/ documentation: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/samtools/mpileup/meta.yml b/software/samtools/mpileup/meta.yml index 5494b13b..7e432a78 100644 --- a/software/samtools/mpileup/meta.yml +++ b/software/samtools/mpileup/meta.yml @@ -14,27 +14,6 @@ tools: homepage: http://www.htslib.org/ documentation: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/samtools/sort/meta.yml b/software/samtools/sort/meta.yml index d87bf858..704e8c1f 100644 --- a/software/samtools/sort/meta.yml +++ b/software/samtools/sort/meta.yml @@ -14,27 +14,6 @@ tools: homepage: http://www.htslib.org/ documentation: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/samtools/stats/meta.yml b/software/samtools/stats/meta.yml index b907df92..b549ff5c 100644 --- a/software/samtools/stats/meta.yml +++ b/software/samtools/stats/meta.yml @@ -15,27 +15,6 @@ tools: homepage: http://www.htslib.org/ documentation: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/samtools/view/meta.yml b/software/samtools/view/meta.yml index 773b40b1..c35a8b03 100644 --- a/software/samtools/view/meta.yml +++ b/software/samtools/view/meta.yml @@ -14,27 +14,6 @@ tools: homepage: http://www.htslib.org/ documentation: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/seacr/callpeak/meta.yml b/software/seacr/callpeak/meta.yml index f95725c9..579961e2 100644 --- a/software/seacr/callpeak/meta.yml +++ b/software/seacr/callpeak/meta.yml @@ -16,27 +16,6 @@ tools: (i.e. regions with no read coverage). homepage: https://github.com/FredHutch/SEACR documentation: https://github.com/FredHutch/SEACR -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/seqkit/split2/meta.yml b/software/seqkit/split2/meta.yml index f0868f93..44ae4ea7 100644 --- a/software/seqkit/split2/meta.yml +++ b/software/seqkit/split2/meta.yml @@ -10,27 +10,6 @@ tools: homepage: https://github.com/shenwei356/seqkit documentation: https://bioinf.shenwei.me/seqkit/ doi: 10.1371/journal.pone.0163962 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/seqwish/induce/meta.yml b/software/seqwish/induce/meta.yml index 47bb5ac6..0b6b4b5b 100644 --- a/software/seqwish/induce/meta.yml +++ b/software/seqwish/induce/meta.yml @@ -13,27 +13,6 @@ tools: sequences to a variation graph encoding the sequences and their alignments. homepage: https://github.com/ekg/seqwish documentation: https://github.com/ekg/seqwish -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/star/align/meta.yml b/software/star/align/meta.yml index 554fc55c..01bc2ecf 100644 --- a/software/star/align/meta.yml +++ b/software/star/align/meta.yml @@ -13,28 +13,6 @@ tools: homepage: https://github.com/alexdobin/STAR manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf doi: 10.1093/bioinformatics/bts635 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. - input: - meta: type: map diff --git a/software/star/genomegenerate/meta.yml b/software/star/genomegenerate/meta.yml index 59bb0fdd..aae0219b 100644 --- a/software/star/genomegenerate/meta.yml +++ b/software/star/genomegenerate/meta.yml @@ -13,28 +13,6 @@ tools: homepage: https://github.com/alexdobin/STAR manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf doi: 10.1093/bioinformatics/bts635 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. - input: - fasta: type: file diff --git a/software/tabix/bgzip/meta.yml b/software/tabix/bgzip/meta.yml index 2bdb2a0f..686d72e6 100644 --- a/software/tabix/bgzip/meta.yml +++ b/software/tabix/bgzip/meta.yml @@ -11,27 +11,6 @@ tools: homepage: https://www.htslib.org/doc/tabix.html documentation: http://www.htslib.org/doc/bgzip.html doi: 10.1093/bioinformatics/btp352 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/tabix/tabix/meta.yml b/software/tabix/tabix/meta.yml index 8075184a..f66270db 100644 --- a/software/tabix/tabix/meta.yml +++ b/software/tabix/tabix/meta.yml @@ -10,27 +10,6 @@ tools: homepage: https://www.htslib.org/doc/tabix.html documentation: https://www.htslib.org/doc/tabix.1.html doi: 10.1093/bioinformatics/btq671 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/tiddit/sv/meta.yml b/software/tiddit/sv/meta.yml index 0ecd809b..f1601f72 100644 --- a/software/tiddit/sv/meta.yml +++ b/software/tiddit/sv/meta.yml @@ -10,27 +10,6 @@ tools: homepage: https://github.com/SciLifeLab/TIDDIT documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md doi: 10.12688/f1000research.11168.1 -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - meta: type: map diff --git a/software/trimgalore/meta.yml b/software/trimgalore/meta.yml index 86ba5cd4..73538707 100644 --- a/software/trimgalore/meta.yml +++ b/software/trimgalore/meta.yml @@ -13,47 +13,6 @@ tools: MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. - - clip_r1: - type: integer - description: | - Instructs Trim Galore to remove bp from the 5' end of read 1 - (or single-end reads) - - clip_r2: - type: integer - description: | - Instructs Trim Galore to remove bp from the 5' end of read 2 - (paired-end reads only) - - three_prime_clip_r1: - type: integer - description: | - Instructs Trim Galore to remove bp from the 3' end of read 1 - AFTER adapter/quality trimming has been performed - - three_prime_clip_r2: - type: integer - description: | - Instructs Trim Galore to re move bp from the 3' end of read 2 - AFTER adapter/quality trimming has been performed input: - meta: type: map diff --git a/software/untar/meta.yml b/software/untar/meta.yml index 32d03b94..af4674f0 100644 --- a/software/untar/meta.yml +++ b/software/untar/meta.yml @@ -8,27 +8,6 @@ tools: description: | Extract tar.gz files. documentation: https://www.gnu.org/software/tar/manual/ -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - publish_dir_mode: - type: string - description: | - Value for the Nextflow `publishDir` mode parameter. - Available: symlink, rellink, link, copy, copyNoFollow, move. - - enable_conda: - type: boolean - description: | - Run the module with Conda using the software specified - via the `conda` directive - - singularity_pull_docker_container: - type: boolean - description: | - Instead of directly downloading Singularity images for use with Singularity, - force the workflow to pull and convert Docker containers instead. input: - archive: type: file