Merge pull request nf-core#293 from JoseEspinosa/updates

Update modules and subworkflows
ktrns · Jun 14, 2023 · eb04c86 · eb04c86
2 parents b7d9871 + d781ad5
commit eb04c86
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Showing 13 changed files with 81 additions and 31 deletions.
diff --git a/modules.json b/modules.json
@@ -17,12 +17,12 @@
                     },
                     "bowtie2/align": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
-                        "installed_by": ["fastq_align_bowtie2", "modules"]
+                        "git_sha": "fe54581f8bed20e4c4a51c616c93fd3379d89820",
+                        "installed_by": ["modules", "fastq_align_bowtie2"]
                     },
                     "bowtie2/build": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "6a24fbe314bb2e6fe6306c29a63076ea87e8eb3c",
                         "installed_by": ["modules"]
                     },
                     "bwa/index": {
@@ -112,7 +112,7 @@
                     },
                     "picard/markduplicates": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
                         "installed_by": ["bam_markduplicates_picard", "modules"]
                     },
                     "picard/mergesamfiles": {
@@ -142,13 +142,13 @@
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
                         "installed_by": ["bam_sort_stats_samtools", "modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["bam_stats_samtools", "modules"]
+                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
+                        "installed_by": ["modules", "bam_stats_samtools"]
                     },
                     "subread/featurecounts": {
                         "branch": "master",
@@ -186,7 +186,7 @@
                     },
                     "bam_sort_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
+                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
                         "installed_by": [
                             "fastq_align_bowtie2",
                             "fastq_align_bwa",
@@ -196,8 +196,8 @@
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
-                        "installed_by": ["bam_sort_stats_samtools", "subworkflows", "bam_markduplicates_picard"]
+                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
+                        "installed_by": ["bam_markduplicates_picard", "subworkflows", "bam_sort_stats_samtools"]
                     },
                     "fastq_align_bowtie2": {
                         "branch": "master",

diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf
diff --git a/modules/nf-core/bowtie2/align/meta.yml b/modules/nf-core/bowtie2/align/meta.yml
diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf
diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf
diff --git a/modules/nf-core/picard/markduplicates/meta.yml b/modules/nf-core/picard/markduplicates/meta.yml
diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf
diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml
diff --git a/subworkflows/nf-core/bam_markduplicates_picard/main.nf b/subworkflows/nf-core/bam_markduplicates_picard/main.nf
diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf
diff --git a/subworkflows/nf-core/bam_stats_samtools/main.nf b/subworkflows/nf-core/bam_stats_samtools/main.nf
diff --git a/subworkflows/nf-core/fastq_align_bowtie2/main.nf b/subworkflows/nf-core/fastq_align_bowtie2/main.nf