Run nf-core modules update

nf-core · Feb 14, 2022 · 01de13e · 01de13e
1 parent 684b4f4
commit 01de13e
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Showing 40 changed files with 186 additions and 53 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -5,11 +5,11 @@ lint:
     - lib/NfcoreTemplate.groovy
 update:
   nf-core/modules:
-    rseqc/bamstat: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/inferexperiment: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/innerdistance: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/junctionannotation: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/junctionsaturation: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/readdistribution: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/readduplication: "9d0cad583b9a71a6509b754fdf589cbfbed08961"
-    rseqc/tin: "ce8c781bb494c2cc1f0a951c31c7b2f4af12e8af"
+    rseqc/bamstat: "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+    rseqc/inferexperiment: "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+    rseqc/innerdistance: "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+    rseqc/junctionannotation: "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+    rseqc/junctionsaturation: "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+    rseqc/readdistribution: "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+    rseqc/readduplication: "e20e57f90b6787ac9a010a980cf6ea98bd990046"
+    rseqc/tin: "e20e57f90b6787ac9a010a980cf6ea98bd990046"
diff --git a/modules.json b/modules.json
@@ -4,118 +4,118 @@
     "repos": {
         "nf-core/modules": {
             "bbmap/bbsplit": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "cat/fastq": {
-                "git_sha": "826a5603db5cf5b4f1e55cef9cc0b7c37d3c7e70"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "custom/dumpsoftwareversions": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "fastqc": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "gffread": {
-                "git_sha": "d473a247d2e0c619b0df877ea19d9a5a98c8e3c8"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "gunzip": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "hisat2/align": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "hisat2/build": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "hisat2/extractsplicesites": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "picard/markduplicates": {
-                "git_sha": "0d1e21686a586447b7592e40da9b3a7cdeedf03c"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "preseq/lcextrap": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "qualimap/rnaseq": {
-                "git_sha": "d473a247d2e0c619b0df877ea19d9a5a98c8e3c8"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rsem/calculateexpression": {
-                "git_sha": "d473a247d2e0c619b0df877ea19d9a5a98c8e3c8"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rsem/preparereference": {
-                "git_sha": "47a9cf8ecbe4de4dcb8b9cc6731fece82b934ab7"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rseqc/bamstat": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rseqc/inferexperiment": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rseqc/innerdistance": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rseqc/junctionannotation": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rseqc/junctionsaturation": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rseqc/readdistribution": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rseqc/readduplication": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "rseqc/tin": {
-                "git_sha": "ce8c781bb494c2cc1f0a951c31c7b2f4af12e8af"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "salmon/index": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "salmon/quant": {
-                "git_sha": "d473a247d2e0c619b0df877ea19d9a5a98c8e3c8"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "samtools/flagstat": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "samtools/idxstats": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "samtools/index": {
-                "git_sha": "0fafaeebf52cc5ab554b83297ed02a48d852a848"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "samtools/sort": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "samtools/stats": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "sortmerna": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "stringtie/stringtie": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "subread/featurecounts": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "trimgalore": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "ucsc/bedclip": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "ucsc/bedgraphtobigwig": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "umitools/dedup": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "umitools/extract": {
-                "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             },
             "untar": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
+                "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
             }
         }
     }

diff --git a/modules/nf-core/modules/bbmap/bbsplit/main.nf b/modules/nf-core/modules/bbmap/bbsplit/main.nf
diff --git a/modules/nf-core/modules/cat/fastq/main.nf b/modules/nf-core/modules/cat/fastq/main.nf
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
diff --git a/modules/nf-core/modules/fastqc/main.nf b/modules/nf-core/modules/fastqc/main.nf
diff --git a/modules/nf-core/modules/gffread/main.nf b/modules/nf-core/modules/gffread/main.nf
diff --git a/modules/nf-core/modules/gunzip/main.nf b/modules/nf-core/modules/gunzip/main.nf
diff --git a/modules/nf-core/modules/hisat2/align/main.nf b/modules/nf-core/modules/hisat2/align/main.nf
diff --git a/modules/nf-core/modules/hisat2/build/main.nf b/modules/nf-core/modules/hisat2/build/main.nf
diff --git a/modules/nf-core/modules/hisat2/extractsplicesites/main.nf b/modules/nf-core/modules/hisat2/extractsplicesites/main.nf
diff --git a/modules/nf-core/modules/picard/markduplicates/main.nf b/modules/nf-core/modules/picard/markduplicates/main.nf
diff --git a/modules/nf-core/modules/preseq/lcextrap/main.nf b/modules/nf-core/modules/preseq/lcextrap/main.nf
diff --git a/modules/nf-core/modules/qualimap/rnaseq/main.nf b/modules/nf-core/modules/qualimap/rnaseq/main.nf
diff --git a/modules/nf-core/modules/rsem/calculateexpression/main.nf b/modules/nf-core/modules/rsem/calculateexpression/main.nf
diff --git a/modules/nf-core/modules/rsem/preparereference/main.nf b/modules/nf-core/modules/rsem/preparereference/main.nf
diff --git a/modules/nf-core/modules/rseqc/bamstat/main.nf b/modules/nf-core/modules/rseqc/bamstat/main.nf
diff --git a/modules/nf-core/modules/rseqc/inferexperiment/main.nf b/modules/nf-core/modules/rseqc/inferexperiment/main.nf
diff --git a/modules/nf-core/modules/rseqc/innerdistance/main.nf b/modules/nf-core/modules/rseqc/innerdistance/main.nf
diff --git a/modules/nf-core/modules/rseqc/junctionannotation/main.nf b/modules/nf-core/modules/rseqc/junctionannotation/main.nf
diff --git a/modules/nf-core/modules/rseqc/junctionsaturation/main.nf b/modules/nf-core/modules/rseqc/junctionsaturation/main.nf
diff --git a/modules/nf-core/modules/rseqc/readdistribution/main.nf b/modules/nf-core/modules/rseqc/readdistribution/main.nf