From 890e002ca5da830ca2d8eae56be3f128ac7395d2 Mon Sep 17 00:00:00 2001 From: Roberto Rossini <71787608+robomics@users.noreply.github.com> Date: Sat, 26 Aug 2023 19:22:52 +0200 Subject: [PATCH] Workaround bug in chromap See https://github.com/nf-core/chipseq/issues/291 --- configs/nfcore/nfcore_chipseq_ctcf.json | 2 +- configs/nfcore/nfcore_chipseq_gh2ax.json | 2 +- configs/nfcore/nfcore_chipseq_h2az.json | 2 +- configs/nfcore/nfcore_chipseq_h3k27ac.json | 2 +- configs/nfcore/nfcore_chipseq_h3k9ac.json | 2 +- configs/nfcore/nfcore_chipseq_h3k9me3.json | 2 +- configs/nfcore/nfcore_chipseq_h3kxxme.json | 2 +- configs/nfcore/nfcore_chipseq_p53.json | 2 +- run_postprocess_nfcore_hic.sh | 18 ------------------ run_postprocess_nfcore_rnaseq.sh | 18 ------------------ 10 files changed, 8 insertions(+), 44 deletions(-) delete mode 100755 run_postprocess_nfcore_hic.sh delete mode 100755 run_postprocess_nfcore_rnaseq.sh diff --git a/configs/nfcore/nfcore_chipseq_ctcf.json b/configs/nfcore/nfcore_chipseq_ctcf.json index 23fc46a..5543420 100644 --- a/configs/nfcore/nfcore_chipseq_ctcf.json +++ b/configs/nfcore/nfcore_chipseq_ctcf.json @@ -3,7 +3,7 @@ "outdir": "data/output/nfcore_chipseq/ctcf", "fasta": "data/input/hg38/hg38.fa", "gtf": "data/input/hg38/hg38_gencode_v43.gtf", - "aligner": "chromap", + "aligner": "bwa", "macs_gsize": 2820945813, "macs_gsize_comment_": "Computed with unique-kmers.py from khmer v2.1.1 (using -k 100)", "narrow_peak": true, diff --git a/configs/nfcore/nfcore_chipseq_gh2ax.json b/configs/nfcore/nfcore_chipseq_gh2ax.json index a4fa6ab..396f66d 100644 --- a/configs/nfcore/nfcore_chipseq_gh2ax.json +++ b/configs/nfcore/nfcore_chipseq_gh2ax.json @@ -3,7 +3,7 @@ "outdir": "data/output/nfcore_chipseq/gh2ax", "fasta": "data/input/hg38/hg38.fa", "gtf": "data/input/hg38/hg38_gencode_v43.gtf", - "aligner": "chromap", + "aligner": "bwa", "macs_gsize": 2708135512, "macs_gsize_comment_": "Computed with unique-kmers.py from khmer v2.1.1 (using -k 50)", "schema_ignore_params": "cluster-options,clusterOptions,genomes,macs_gsize_comment_,project" diff --git a/configs/nfcore/nfcore_chipseq_h2az.json b/configs/nfcore/nfcore_chipseq_h2az.json index 46e18d9..9c879e8 100644 --- a/configs/nfcore/nfcore_chipseq_h2az.json +++ b/configs/nfcore/nfcore_chipseq_h2az.json @@ -3,7 +3,7 @@ "outdir": "data/output/nfcore_chipseq/h2az", "fasta": "data/input/hg38/hg38.fa", "gtf": "data/input/hg38/hg38_gencode_v43.gtf", - "aligner": "chromap", + "aligner": "bwa", "macs_gsize": 2708135512, "macs_gsize_comment_": "Computed with unique-kmers.py from khmer v2.1.1 (using -k 50)", "schema_ignore_params": "cluster-options,clusterOptions,genomes,macs_gsize_comment_,project" diff --git a/configs/nfcore/nfcore_chipseq_h3k27ac.json b/configs/nfcore/nfcore_chipseq_h3k27ac.json index 371f5b6..6a343d9 100644 --- a/configs/nfcore/nfcore_chipseq_h3k27ac.json +++ b/configs/nfcore/nfcore_chipseq_h3k27ac.json @@ -3,7 +3,7 @@ "outdir": "data/output/nfcore_chipseq/h3k27ac", "fasta": "data/input/hg38/hg38.fa", "gtf": "data/input/hg38/hg38_gencode_v43.gtf", - "aligner": "chromap", + "aligner": "bwa", "macs_gsize": 2765359936, "macs_gsize_comment": "Computed with unique-kmers.py from khmer v2.1.1 (using -k 75)", "schema_ignore_params": "cluster-options,clusterOptions,genomes,macs_gsize_comment_,project" diff --git a/configs/nfcore/nfcore_chipseq_h3k9ac.json b/configs/nfcore/nfcore_chipseq_h3k9ac.json index 481b7c4..19569c1 100644 --- a/configs/nfcore/nfcore_chipseq_h3k9ac.json +++ b/configs/nfcore/nfcore_chipseq_h3k9ac.json @@ -3,7 +3,7 @@ "outdir": "data/output/nfcore_chipseq/h3k9ac", "fasta": "data/input/hg38/hg38.fa", "gtf": "data/input/hg38/hg38_gencode_v43.gtf", - "aligner": "chromap", + "aligner": "bwa", "macs_gsize": 2573408389, "macs_gsize_comment_": "Computed with unique-kmers.py from khmer v2.1.1 (using -k 35)", "schema_ignore_params": "cluster-options,clusterOptions,genomes,macs_gsize_comment_,project" diff --git a/configs/nfcore/nfcore_chipseq_h3k9me3.json b/configs/nfcore/nfcore_chipseq_h3k9me3.json index 449c6f4..e1a8d10 100644 --- a/configs/nfcore/nfcore_chipseq_h3k9me3.json +++ b/configs/nfcore/nfcore_chipseq_h3k9me3.json @@ -3,7 +3,7 @@ "outdir": "data/output/nfcore_chipseq/h3k9me3", "fasta": "data/input/hg38/hg38.fa", "gtf": "data/input/hg38/hg38_gencode_v43.gtf", - "aligner": "chromap", + "aligner": "bwa", "macs_gsize": 2573408389, "macs_gsize_comment_": "Computed with unique-kmers.py from khmer v2.1.1 (using -k 35)", "schema_ignore_params": "cluster-options,clusterOptions,genomes,macs_gsize_comment_,project" diff --git a/configs/nfcore/nfcore_chipseq_h3kxxme.json b/configs/nfcore/nfcore_chipseq_h3kxxme.json index 2ed34b6..ca62f7a 100644 --- a/configs/nfcore/nfcore_chipseq_h3kxxme.json +++ b/configs/nfcore/nfcore_chipseq_h3kxxme.json @@ -3,7 +3,7 @@ "outdir": "data/output/nfcore_chipseq/h3kxxme", "fasta": "data/input/hg38/hg38.fa", "gtf": "data/input/hg38/hg38_gencode_v43.gtf", - "aligner": "chromap", + "aligner": "bwa", "macs_gsize": 2636580800, "macs_gsize_comment_": "Computed with unique-kmers.py from khmer v2.1.1 (using -k 40)", "schema_ignore_params": "cluster-options,clusterOptions,genomes,macs_gsize_comment_,project" diff --git a/configs/nfcore/nfcore_chipseq_p53.json b/configs/nfcore/nfcore_chipseq_p53.json index ef73f9a..0c05096 100644 --- a/configs/nfcore/nfcore_chipseq_p53.json +++ b/configs/nfcore/nfcore_chipseq_p53.json @@ -3,7 +3,7 @@ "outdir": "data/output/nfcore_chipseq/p53", "fasta": "data/input/hg38/hg38.fa", "gtf": "data/input/hg38/hg38_gencode_v43.gtf", - "aligner": "chromap", + "aligner": "bwa", "macs_gsize": 2802903967, "macs_gsize_comment_": "Computed with unique-kmers.py from khmer v2.1.1 (using -k 80)", "narrow_peak": true, diff --git a/run_postprocess_nfcore_hic.sh b/run_postprocess_nfcore_hic.sh deleted file mode 100755 index cca9141..0000000 --- a/run_postprocess_nfcore_hic.sh +++ /dev/null @@ -1,18 +0,0 @@ -#!/usr/bin/env bash - -# Copyright (C) 2022 Roberto Rossini -# -# SPDX-License-Identifier: MIT - -set -e -set -u -set -o pipefail -set -x - - -step='postprocess_nfcore_hic' -wd=".nextflow-$step-wd" -mkdir -p "$wd" - -./setup_workflow_workdir.sh "$PWD" "$wd" -./run_workflow.sh "$wd" "$step" diff --git a/run_postprocess_nfcore_rnaseq.sh b/run_postprocess_nfcore_rnaseq.sh deleted file mode 100755 index d7080ae..0000000 --- a/run_postprocess_nfcore_rnaseq.sh +++ /dev/null @@ -1,18 +0,0 @@ -#!/usr/bin/env bash - -# Copyright (C) 2022 Roberto Rossini -# -# SPDX-License-Identifier: MIT - -set -e -set -u -set -o pipefail -set -x - - -step='postprocess_nfcore_rnaseq' -wd=".nextflow-$step-wd" -mkdir -p "$wd" - -./setup_workflow_workdir.sh "$PWD" "$wd" -./run_workflow.sh "$wd" "$step"