Workaround bug in chromap

See nf-core/chipseq#291
paulsengroup · Aug 26, 2023 · 890e002 · 890e002
1 parent 363e6dd
commit 890e002
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Showing 10 changed files with 8 additions and 44 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
diff --git a/run_postprocess_nfcore_rnaseq.sh b/run_postprocess_nfcore_rnaseq.sh