Merge pull request #521 from maxulysse/dev_modules_die_samtools_local…

…_die Move most of local modules to nf-core modules
nf-core · Apr 27, 2022 · 9c57179 · 9c57179
2 parents c31f1f8 + f540226
commit 9c57179
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Showing 37 changed files with 401 additions and 551 deletions.
diff --git a/conf/modules.config b/conf/modules.config
diff --git a/modules.json b/modules.json
@@ -174,6 +174,12 @@
             "samtools/bam2fq": {
                 "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
             },
+            "samtools/bamtocram": {
+                "git_sha": "569e07f0af74e2a6ea43fca61ae90bb762893461"
+            },
+            "samtools/collatefastq": {
+                "git_sha": "705f8c9ac4dfdf07666e71abde28f267e2dfd5eb"
+            },
             "samtools/faidx": {
                 "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
             },
@@ -204,6 +210,9 @@
             "strelka/somatic": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
+            "tabix/bgzip": {
+                "git_sha": "37bf3936f3665483d070a5e0e0b314311032af7c"
+            },
             "tabix/bgziptabix": {
                 "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
             },

diff --git a/modules/local/samtools/index/main.nf b/modules/local/samtools/index/main.nf
diff --git a/modules/local/samtools/index/meta.yml b/modules/local/samtools/index/meta.yml
diff --git a/modules/local/samtools/mergecram/main.nf b/modules/local/samtools/mergecram/main.nf
diff --git a/modules/local/samtools/viewindex/meta.yml b/modules/local/samtools/viewindex/meta.yml
diff --git a/modules/local/samtoolsview.nf b/modules/local/samtoolsview.nf
diff --git a/modules/local/samtools/viewindex/main.nf → ...f-core/modules/samtools/bamtocram/main.nf b/modules/local/samtools/viewindex/main.nf → ...f-core/modules/samtools/bamtocram/main.nf
diff --git a/modules/local/samtools/mergecram/meta.yml → ...-core/modules/samtools/bamtocram/meta.yml b/modules/local/samtools/mergecram/meta.yml → ...-core/modules/samtools/bamtocram/meta.yml
diff --git a/modules/local/samtools/fastq/main.nf → ...ore/modules/samtools/collatefastq/main.nf b/modules/local/samtools/fastq/main.nf → ...ore/modules/samtools/collatefastq/main.nf