Merge pull request #30 from ramprasadn/modulesupdate

update modules
nf-core · Jun 11, 2024 · a0333ea · a0333ea
2 parents 86b516b + 6b48b13
commit a0333ea
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Showing 66 changed files with 2,080 additions and 132 deletions.
diff --git a/modules.json b/modules.json
@@ -7,27 +7,27 @@
                 "nf-core": {
                     "cnvkit/batch": {
                         "branch": "master",
-                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
+                        "git_sha": "f53b071421340e6fac0806c86ba030e578e94826",
                         "installed_by": ["modules"]
                     },
                     "gatk4/annotateintervals": {
                         "branch": "master",
-                        "git_sha": "42ae163c3c6eb23646189c30c07a889ad39c9b0e",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/bedtointervallist": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d3f215802f696f7993f25c759781d2db91232015",
                         "installed_by": ["modules"]
                     },
                     "gatk4/collectreadcounts": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/createreadcountpanelofnormals": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/createsomaticpanelofnormals": {
@@ -37,12 +37,12 @@
                     },
                     "gatk4/determinegermlinecontigploidy": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "60a7dbae179bcfa24c10294cc9a07423a239c19a",
                         "installed_by": ["modules"]
                     },
                     "gatk4/filterintervals": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/genomicsdbimport": {
@@ -52,32 +52,32 @@
                     },
                     "gatk4/germlinecnvcaller": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "cf607b7749da0a8f5ca2a1e31233e13e3159e2fe",
                         "installed_by": ["modules"]
                     },
                     "gatk4/indexfeaturefile": {
                         "branch": "master",
-                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
+                        "git_sha": "108e1f5bafc045ac19890852a41e8d95ae12aa67",
                         "installed_by": ["modules"]
                     },
                     "gatk4/intervallisttools": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "afb604624abcc2fc67a43d70a2de369a50d16105",
                         "installed_by": ["modules"]
                     },
                     "gatk4/mutect2": {
                         "branch": "master",
-                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
+                        "git_sha": "5fd04feb37b58caa6a54d41e38c80066bdf71056",
                         "installed_by": ["bam_create_som_pon_gatk"]
                     },
                     "gatk4/preprocessintervals": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
+                        "git_sha": "8f2062e7b4185590fb9f43c275381a31a6544fc0",
                         "installed_by": ["modules"]
                     },
                     "picard/createsequencedictionary": {
@@ -87,12 +87,12 @@
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/nf-core/cnvkit/batch/environment.yml b/modules/nf-core/cnvkit/batch/environment.yml
diff --git a/modules/nf-core/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf
diff --git a/modules/nf-core/cnvkit/batch/meta.yml b/modules/nf-core/cnvkit/batch/meta.yml
diff --git a/modules/nf-core/cnvkit/batch/tests/batch_hybrid.config b/modules/nf-core/cnvkit/batch/tests/batch_hybrid.config
diff --git a/modules/nf-core/cnvkit/batch/tests/batch_pon.config b/modules/nf-core/cnvkit/batch/tests/batch_pon.config
diff --git a/modules/nf-core/cnvkit/batch/tests/batch_tumouronly.config b/modules/nf-core/cnvkit/batch/tests/batch_tumouronly.config
diff --git a/modules/nf-core/cnvkit/batch/tests/batch_wgs.config b/modules/nf-core/cnvkit/batch/tests/batch_wgs.config