Switch to subworkflow from nf-core

nf-core · Dec 12, 2024 · 3498463 · 3498463
1 parent 9196038
commit 3498463
Showing 1 changed file with 21 additions and 16 deletions.
diff --git a/modules.json b/modules.json
@@ -190,17 +190,17 @@
                         "installed_by": ["fastq_subsample_fq_salmon", "modules", "quantify_pseudo_alignment"]
                     },
                     "samtools/flagstat": {
-                        "branch": "master",
+                        "branch": "bam_dedup_umi_imports",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/idxstats": {
-                        "branch": "master",
+                        "branch": "bam_dedup_umi_imports",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/index": {
-                        "branch": "master",
+                        "branch": "bam_dedup_umi_imports",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": [
                             "bam_dedup_stats_samtools_umicollapse",
@@ -210,12 +210,12 @@
                         ]
                     },
                     "samtools/sort": {
-                        "branch": "master",
+                        "branch": "bam_dedup_umi_imports",
                         "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
-                        "installed_by": ["bam_sort_stats_samtools"]
+                        "installed_by": ["bam_dedup_umi", "bam_sort_stats_samtools"]
                     },
                     "samtools/stats": {
-                        "branch": "master",
+                        "branch": "bam_dedup_umi_imports",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["bam_stats_samtools"]
                     },
@@ -273,12 +273,12 @@
                         "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
                     },
                     "umicollapse": {
-                        "branch": "master",
+                        "branch": "bam_dedup_umi_imports",
                         "git_sha": "0b27602842d3d79fd0e8db79f4afa764967fc3d1",
                         "installed_by": ["bam_dedup_stats_samtools_umicollapse"]
                     },
                     "umitools/dedup": {
-                        "branch": "master",
+                        "branch": "bam_dedup_umi_imports",
                         "git_sha": "0b27602842d3d79fd0e8db79f4afa764967fc3d1",
                         "installed_by": ["bam_dedup_stats_samtools_umitools"]
                     },
@@ -288,9 +288,9 @@
                         "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
                     },
                     "umitools/prepareforrsem": {
-                        "branch": "master",
+                        "branch": "bam_dedup_umi_imports",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": ["bam_dedup_umi", "modules"]
                     },
                     "untar": {
                         "branch": "master",
@@ -302,13 +302,18 @@
             "subworkflows": {
                 "nf-core": {
                     "bam_dedup_stats_samtools_umicollapse": {
-                        "branch": "master",
+                        "branch": "bam_dedup_umi_imports",
                         "git_sha": "0b27602842d3d79fd0e8db79f4afa764967fc3d1",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": ["bam_dedup_umi", "subworkflows"]
                     },
                     "bam_dedup_stats_samtools_umitools": {
-                        "branch": "master",
+                        "branch": "bam_dedup_umi_imports",
                         "git_sha": "0b27602842d3d79fd0e8db79f4afa764967fc3d1",
+                        "installed_by": ["bam_dedup_umi", "subworkflows"]
+                    },
+                    "bam_dedup_umi": {
+                        "branch": "bam_dedup_umi_imports",
+                        "git_sha": "0f24ce2f41bbc71fea83ffb8425c3ea0d9a75abb",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_markduplicates_picard": {
@@ -322,12 +327,12 @@
                         "installed_by": ["subworkflows"]
                     },
                     "bam_sort_stats_samtools": {
-                        "branch": "master",
+                        "branch": "bam_dedup_umi_imports",
                         "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
-                        "installed_by": ["fastq_align_hisat2"]
+                        "installed_by": ["bam_dedup_umi", "fastq_align_hisat2"]
                     },
                     "bam_stats_samtools": {
-                        "branch": "master",
+                        "branch": "bam_dedup_umi_imports",
                         "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d",
                         "installed_by": [
                             "bam_dedup_stats_samtools_umicollapse",