updated all modules

nf-core · Feb 2, 2024 · 0ae2212 · 0ae2212
1 parent 8525c68
commit 0ae2212
Show file tree

Hide file tree

Showing 121 changed files with 2,869 additions and 341 deletions.
diff --git a/modules.json b/modules.json
@@ -7,92 +7,92 @@
                 "nf-core": {
                     "bwa/aln": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["fastq_align_bwaaln", "modules"]
                     },
                     "bwa/index": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "bwa/sampe": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "git_sha": "1e2b7fb7106852388610c0360d234b0829eb980e",
                         "installed_by": ["fastq_align_bwaaln"]
                     },
                     "bwa/samse": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "git_sha": "1e2b7fb7106852388610c0360d234b0829eb980e",
                         "installed_by": ["fastq_align_bwaaln"]
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
+                        "git_sha": "02fd5bd7275abad27aad32d5c852e0a9b1b98882",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
                         "installed_by": ["modules"]
                     },
                     "deeptools/bamcoverage": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "102cc9b709a6da9f7cee2373563ab1464fca9c0a",
+                        "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
+                        "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
+                        "git_sha": "9e71d8519dfbfc328c078bba14d4bd4c99e39a94",
                         "installed_by": ["modules"]
                     },
                     "picard/markduplicates": {
                         "branch": "master",
-                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
+                        "git_sha": "ec833ac4c29db6005d18baccf3306f557c46b006",
                         "installed_by": ["bam_markduplicates_picard", "modules"]
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
+                        "git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
                         "installed_by": ["modules"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c",
+                        "git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639",
+                        "git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
                         "installed_by": ["bam_markduplicates_picard", "fastq_align_bwaaln"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
+                        "git_sha": "ec833ac4c29db6005d18baccf3306f557c46b006",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "trimmomatic": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
+                        "git_sha": "e719354ba77df0a1bd310836aa2039b45c29d620",
                         "installed_by": ["modules"]
                     }
                 }
@@ -101,17 +101,17 @@
                 "nf-core": {
                     "bam_markduplicates_picard": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
                         "installed_by": ["bam_markduplicates_picard"]
                     },
                     "fastq_align_bwaaln": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
                         "installed_by": ["subworkflows"]
                     }
                 }

diff --git a/modules/nf-core/bwa/aln/environment.yml b/modules/nf-core/bwa/aln/environment.yml
diff --git a/modules/nf-core/bwa/aln/main.nf b/modules/nf-core/bwa/aln/main.nf
diff --git a/modules/nf-core/bwa/aln/meta.yml b/modules/nf-core/bwa/aln/meta.yml
diff --git a/modules/nf-core/bwa/aln/tests/main.nf.test b/modules/nf-core/bwa/aln/tests/main.nf.test
diff --git a/modules/nf-core/bwa/aln/tests/main.nf.test.snap b/modules/nf-core/bwa/aln/tests/main.nf.test.snap
diff --git a/modules/nf-core/bwa/aln/tests/tags.yml b/modules/nf-core/bwa/aln/tests/tags.yml
diff --git a/modules/nf-core/bwa/index/environment.yml b/modules/nf-core/bwa/index/environment.yml
diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf