From 200c946693210698616831293473ff9d2c9522ac Mon Sep 17 00:00:00 2001 From: drpatelh Date: Mon, 14 Dec 2020 00:34:24 +0000 Subject: [PATCH] Add --singularity_pull_docker_container to module yml --- software/SOFTWARE/TOOL/meta.yml | 5 +++++ software/bwa/index/meta.yml | 5 +++++ software/bwa/mem/meta.yml | 5 +++++ software/fastqc/meta.yml | 5 +++++ software/multiqc/meta.yml | 5 +++++ software/picard/collectmultiplemetrics/meta.yml | 5 +++++ software/picard/markduplicates/meta.yml | 5 +++++ software/picard/mergesamfiles/meta.yml | 5 +++++ software/samtools/flagstat/meta.yml | 5 +++++ software/samtools/idxstats/meta.yml | 5 +++++ software/samtools/index/meta.yml | 5 +++++ software/samtools/sort/meta.yml | 5 +++++ software/samtools/stats/meta.yml | 5 +++++ software/trimgalore/meta.yml | 5 +++++ 14 files changed, 70 insertions(+) diff --git a/software/SOFTWARE/TOOL/meta.yml b/software/SOFTWARE/TOOL/meta.yml index 3fd42a5c..e96b6542 100644 --- a/software/SOFTWARE/TOOL/meta.yml +++ b/software/SOFTWARE/TOOL/meta.yml @@ -37,6 +37,11 @@ params: 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. ## TODO nf-core: Add a description of all of the variables used as input input: - meta: diff --git a/software/bwa/index/meta.yml b/software/bwa/index/meta.yml index 973a18db..0c3b8f5f 100644 --- a/software/bwa/index/meta.yml +++ b/software/bwa/index/meta.yml @@ -29,6 +29,11 @@ params: 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 142a5a0e..de61798b 100644 --- a/software/bwa/mem/meta.yml +++ b/software/bwa/mem/meta.yml @@ -32,6 +32,11 @@ params: 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 337fc372..413aad8d 100644 --- a/software/fastqc/meta.yml +++ b/software/fastqc/meta.yml @@ -31,6 +31,11 @@ params: 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 684ccd5e..02f4b415 100644 --- a/software/multiqc/meta.yml +++ b/software/multiqc/meta.yml @@ -27,6 +27,11 @@ params: 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/picard/collectmultiplemetrics/meta.yml b/software/picard/collectmultiplemetrics/meta.yml index 6f2fd8bc..acdbdfec 100644 --- a/software/picard/collectmultiplemetrics/meta.yml +++ b/software/picard/collectmultiplemetrics/meta.yml @@ -30,6 +30,11 @@ params: 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 a91616d8..d9d8619a 100644 --- a/software/picard/markduplicates/meta.yml +++ b/software/picard/markduplicates/meta.yml @@ -30,6 +30,11 @@ params: 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 f47fa903..090432b7 100644 --- a/software/picard/mergesamfiles/meta.yml +++ b/software/picard/mergesamfiles/meta.yml @@ -28,6 +28,11 @@ params: 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/flagstat/meta.yml b/software/samtools/flagstat/meta.yml index 6703c392..a140c795 100644 --- a/software/samtools/flagstat/meta.yml +++ b/software/samtools/flagstat/meta.yml @@ -32,6 +32,11 @@ params: 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 c33f1724..6ff30433 100644 --- a/software/samtools/idxstats/meta.yml +++ b/software/samtools/idxstats/meta.yml @@ -33,6 +33,11 @@ params: 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 8d3e049c..089a83be 100644 --- a/software/samtools/index/meta.yml +++ b/software/samtools/index/meta.yml @@ -30,6 +30,11 @@ params: 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 e8f74b26..d87bf858 100644 --- a/software/samtools/sort/meta.yml +++ b/software/samtools/sort/meta.yml @@ -30,6 +30,11 @@ params: 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 9f478cc0..b907df92 100644 --- a/software/samtools/stats/meta.yml +++ b/software/samtools/stats/meta.yml @@ -31,6 +31,11 @@ params: 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 bc1179e0..86ba5cd4 100644 --- a/software/trimgalore/meta.yml +++ b/software/trimgalore/meta.yml @@ -29,6 +29,11 @@ params: 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: |