From 8b5b635b31d28a128ba574827d841dda7eb31b08 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 10 Sep 2024 15:43:18 +0200 Subject: [PATCH] Remove porechop_abi patch --- modules.json | 227 +++++++++++++----- modules/nf-core/porechop/abi/main.nf | 7 +- .../nf-core/porechop/abi/porechop-abi.diff | 21 -- 3 files changed, 170 insertions(+), 85 deletions(-) delete mode 100644 modules/nf-core/porechop/abi/porechop-abi.diff diff --git a/modules.json b/modules.json index e0651fe0..149fefe4 100644 --- a/modules.json +++ b/modules.json @@ -8,269 +8,374 @@ "adapterremoval": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bbmap/bbduk": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bowtie2/align": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bowtie2/build": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bracken/bracken": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bracken/combinebrackenoutputs": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/fastq": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "centrifuge/centrifuge": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "centrifuge/kreport": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "diamond/blastx": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "falco": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "fastp": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "fastqc": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "filtlong": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ganon/classify": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ganon/report": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ganon/table": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gunzip": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "kaiju/kaiju": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "kaiju/kaiju2krona": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "kaiju/kaiju2table": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "kmcp/profile": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "kmcp/search": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "kraken2/kraken2": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "krakentools/combinekreports": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "krakentools/kreport2krona": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "krakenuniq/preloadedkrakenuniq": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "krona/ktimporttaxonomy": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "krona/ktimporttext": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "malt/run": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "megan/rma2info": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "metaphlan/mergemetaphlantables": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "metaphlan/metaphlan": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "minimap2/align": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "minimap2/index": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "motus/merge": { "branch": "master", "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "motus/profile": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "nanoq": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "nonpareil/curve": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "nonpareil/nonpareil": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "nonpareil/nonpareilcurvesr": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "nonpareil/set": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "porechop/abi": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"], - "patch": "modules/nf-core/porechop/abi/porechop-abi.diff" + "installed_by": [ + "modules" + ] }, "porechop/porechop": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/porechop/porechop/porechop-porechop.diff" }, "prinseqplusplus": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/fastq": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/index": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/stats": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/view": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "taxpasta/merge": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "taxpasta/standardise": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "untar": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -279,20 +384,26 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/porechop/abi/main.nf b/modules/nf-core/porechop/abi/main.nf index e9fa9e91..88ec5bd0 100644 --- a/modules/nf-core/porechop/abi/main.nf +++ b/modules/nf-core/porechop/abi/main.nf @@ -22,14 +22,9 @@ process PORECHOP_ABI { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}.porechop_abi" if ("$reads" == "${prefix}.fastq.gz") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" - """ - ## To ensure ID matches rest of pipeline based on meta.id rather than input file name - - [[ -f ${prefix}.fastq.gz ]] || ln -s $reads ${prefix}.fastq.gz - porechop_abi \\ - --input ${prefix}.fastq.gz \\ + --input $reads \\ --threads $task.cpus \\ $args \\ --output ${prefix}.fastq.gz \\ diff --git a/modules/nf-core/porechop/abi/porechop-abi.diff b/modules/nf-core/porechop/abi/porechop-abi.diff deleted file mode 100644 index 4aee2e91..00000000 --- a/modules/nf-core/porechop/abi/porechop-abi.diff +++ /dev/null @@ -1,21 +0,0 @@ -Changes in module 'nf-core/porechop/abi' ---- modules/nf-core/porechop/abi/main.nf -+++ modules/nf-core/porechop/abi/main.nf -@@ -22,9 +22,14 @@ - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}.porechop_abi" - if ("$reads" == "${prefix}.fastq.gz") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" -+ - """ -+ ## To ensure ID matches rest of pipeline based on meta.id rather than input file name -+ -+ [[ -f ${prefix}.fastq.gz ]] || ln -s $reads ${prefix}.fastq.gz -+ - porechop_abi \\ -- --input $reads \\ -+ --input ${prefix}.fastq.gz \\ - --threads $task.cpus \\ - $args \\ - --output ${prefix}.fastq.gz \\ - -************************************************************