From bf462dfe612d0cf0718eec2cc40789292d1b948c Mon Sep 17 00:00:00 2001 From: Laurence Kuhlburger Date: Fri, 8 Mar 2024 14:31:06 +0100 Subject: [PATCH] Ran pre commit --- CHANGELOG.md | 2 +- modules.json | 90 ++++++++------------------------ workflows/crisprseq_screening.nf | 2 +- 3 files changed, 25 insertions(+), 69 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0479264f..794ea696 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Added a csv input option for crisprcleanr ([#105](https://github.com/nf-core/crisprseq/pull/105)) - Added a contrasts parameter so the pipeline automatically creates design matrices and MAGeCK MLE ([#109](https://github.com/nf-core/crisprseq/pull/109)) - Added bowtie2 and three prime and five prime adapter trimming ([#103](https://github.com/nf-core/crisprseq/pull/103) and [#123](https://github.com/nf-core/crisprseq/pull/123) -) + ) ### Fixed diff --git a/modules.json b/modules.json index 44d4fbc9..b7928c26 100644 --- a/modules.json +++ b/modules.json @@ -8,164 +8,120 @@ "bowtie2/align": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bowtie2/build": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwa/index": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwa/mem": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "crisprcleanr/normalize": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/crisprcleanr/normalize/crisprcleanr-normalize.diff" }, "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cutadapt": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/cutadapt/cutadapt.diff" }, "fastqc": { "branch": "master", "git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mageck/count": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/mageck/count/mageck-count.diff" }, "mageck/mle": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/mageck/mle/mageck-mle.diff" }, "mageck/test": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/mageck/test/mageck-test.diff" }, "medaka": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/medaka/medaka.diff" }, "minimap2/align": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/minimap2/align/minimap2-align.diff" }, "minimap2/index": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "pear": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "racon": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/index": { "branch": "master", "git_sha": "5394565c5fe4c760e5b35977ec7607c62e81d1f8", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "seqtk/seq": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vsearch/cluster": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/vsearch/cluster/vsearch-cluster.diff" }, "vsearch/sort": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -174,4 +130,4 @@ } } } -} \ No newline at end of file +} diff --git a/workflows/crisprseq_screening.nf b/workflows/crisprseq_screening.nf index 1c6a94a6..a2905b90 100644 --- a/workflows/crisprseq_screening.nf +++ b/workflows/crisprseq_screening.nf @@ -146,7 +146,7 @@ workflow CRISPRSEQ_SCREENING { ch_cutadapt ) CUTADAPT_FIVE_PRIME.out.reads.combine(Channel.value([[]])).set { ch_cutadapt } - ch_cutadapt.map{ meta, fastq, proto -> + ch_cutadapt.map{ meta, fastq, proto -> meta.id = "${meta.id}_trim" [meta, fastq, proto] }.set { ch_cutadapt }