Merge pull request #371 from genomic-medicine-sweden/update_modules

update modules
nf-core · Jul 5, 2023 · c6091f0 · c6091f0
2 parents aedf19c + 56132b1
commit c6091f0
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Showing 15 changed files with 59 additions and 34 deletions.
diff --git a/modules.json b/modules.json
@@ -17,12 +17,12 @@
                     },
                     "bcftools/filter": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "bd4e0df3319c171072d09dade42e3c06fa373779",
                         "installed_by": ["modules"]
                     },
                     "bcftools/merge": {
                         "branch": "master",
-                        "git_sha": "0435e4eebc94e53721c194b2d5d06f455a79e407",
+                        "git_sha": "f7219b428dc69f93aa19f219fb7ce8eae8720400",
                         "installed_by": ["modules"]
                     },
                     "bcftools/norm": {
@@ -82,7 +82,7 @@
                     },
                     "deepvariant": {
                         "branch": "master",
-                        "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
+                        "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b",
                         "installed_by": ["modules"]
                     },
                     "eklipse": {
@@ -97,7 +97,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117",
                         "installed_by": ["modules"]
                     },
                     "gatk4/bedtointervallist": {
@@ -107,7 +107,7 @@
                     },
                     "gatk4/createsequencedictionary": {
                         "branch": "master",
-                        "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
+                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
                         "installed_by": ["modules"]
                     },
                     "gatk4/filtermutectcalls": {
@@ -137,7 +137,7 @@
                     },
                     "gatk4/printreads": {
                         "branch": "master",
-                        "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
+                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
                         "installed_by": ["modules"]
                     },
                     "gatk4/revertsam": {
@@ -152,17 +152,17 @@
                     },
                     "gatk4/selectvariants": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
                         "installed_by": ["modules"]
                     },
                     "gatk4/shiftfasta": {
                         "branch": "master",
-                        "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
+                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
                         "installed_by": ["modules"]
                     },
                     "gatk4/splitintervals": {
                         "branch": "master",
-                        "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
+                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
                         "installed_by": ["modules"]
                     },
                     "gatk4/variantfiltration": {
@@ -212,7 +212,7 @@
                     },
                     "manta/germline": {
                         "branch": "master",
-                        "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
+                        "git_sha": "80dbd95c558a0ebb2123d95f50c093a7f714a0d7",
                         "installed_by": ["modules"]
                     },
                     "mosdepth": {
@@ -297,7 +297,7 @@
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
                         "installed_by": ["modules"]
                     },
                     "samtools/stats": {
@@ -332,7 +332,7 @@
                     },
                     "tabix/bgziptabix": {
                         "branch": "master",
-                        "git_sha": "01b3b2509d76625b6d6cd613b349fb4777712a15",
+                        "git_sha": "591b71642820933dcb3c954c934b397bd00d8e5e",
                         "installed_by": ["modules"]
                     },
                     "tabix/tabix": {
@@ -352,7 +352,7 @@
                     },
                     "ucsc/wigtobigwig": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "66290981ab6038ea86177ade40b9449bc790b0ce",
                         "installed_by": ["modules"]
                     },
                     "untar": {

diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf
diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf
diff --git a/modules/nf-core/deepvariant/main.nf b/modules/nf-core/deepvariant/main.nf
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf
diff --git a/modules/nf-core/gatk4/printreads/main.nf b/modules/nf-core/gatk4/printreads/main.nf
diff --git a/modules/nf-core/gatk4/selectvariants/main.nf b/modules/nf-core/gatk4/selectvariants/main.nf
diff --git a/modules/nf-core/gatk4/shiftfasta/main.nf b/modules/nf-core/gatk4/shiftfasta/main.nf
diff --git a/modules/nf-core/gatk4/splitintervals/main.nf b/modules/nf-core/gatk4/splitintervals/main.nf
diff --git a/modules/nf-core/manta/germline/main.nf b/modules/nf-core/manta/germline/main.nf
diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf
diff --git a/modules/nf-core/ucsc/wigtobigwig/main.nf b/modules/nf-core/ucsc/wigtobigwig/main.nf
diff --git a/modules/nf-core/ucsc/wigtobigwig/meta.yml b/modules/nf-core/ucsc/wigtobigwig/meta.yml