Merge pull request #51 from genomic-medicine-sweden/dev

Dev
genomic-medicine-sweden · Nov 6, 2023 · 963eb95 · 963eb95
2 parents 0ab47a2 + cd90ccd
commit 963eb95
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diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/genomic-medicine-sweden/tomte/releases/tag/dev" target="_blank">genomic-medicine-sweden/tomte</a>
+  This report has been generated by the <a href="https://github.com/genomic-medicine-sweden/tomte/releases/tag/1.0.0" target="_blank">genomic-medicine-sweden/tomte</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://github.com/genomic-medicine-sweden/tomte/blob/master/docs/output.md" target="_blank">documentation</a>.
 report_section_order:

diff --git a/modules.json b/modules.json
@@ -7,153 +7,153 @@
                 "nf-core": {
                     "bcftools/index": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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                         "installed_by": ["modules"]
                     },
                     "bcftools/mpileup": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/bcftools/mpileup/bcftools-mpileup.diff"
                     },
                     "bcftools/stats": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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                     },
                     "bcftools/view": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
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                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "fc6caedab1c71113aa440900e5989dd1c03ec58f",
                         "installed_by": ["modules"]
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "a33464f205fa15305bfe268546f6607b6f4d4753",
+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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                     },
                     "gatk4/asereadcounter": {
                         "branch": "master",
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                         "installed_by": ["modules"]
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                     "gatk4/bedtointervallist": {
                         "branch": "master",
-                        "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
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                     },
                     "gatk4/createsequencedictionary": {
                         "branch": "master",
-                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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                     },
                     "gatk4/haplotypecaller": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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                     },
                     "gatk4/splitncigarreads": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
                         "installed_by": ["modules"]
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                     "gatk4/variantfiltration": {
                         "branch": "master",
-                        "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
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                     "gffcompare": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
                         "installed_by": ["modules"]
                     },
                     "picard/collectrnaseqmetrics": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
                         "installed_by": ["modules"]
                     },
                     "salmon/index": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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                     },
                     "salmon/quant": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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                         "installed_by": ["modules"]
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
                         "installed_by": ["modules"]
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                     "samtools/view": {
                         "branch": "master",
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                     "star/align": {
                         "branch": "master",
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+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
                         "installed_by": ["modules"]
                     },
                     "star/genomegenerate": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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                     },
                     "stringtie/stringtie": {
                         "branch": "master",
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                     "tabix/bgziptabix": {
                         "branch": "master",
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+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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                     },
                     "tabix/tabix": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
                         "installed_by": ["modules"]
                     },
                     "ucsc/wigtobigwig": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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                         "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
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+                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/nf-core/bcftools/index/environment.yml b/modules/nf-core/bcftools/index/environment.yml
diff --git a/modules/nf-core/bcftools/index/main.nf b/modules/nf-core/bcftools/index/main.nf
diff --git a/modules/nf-core/bcftools/index/meta.yml b/modules/nf-core/bcftools/index/meta.yml
diff --git a/modules/nf-core/bcftools/mpileup/environment.yml b/modules/nf-core/bcftools/mpileup/environment.yml
diff --git a/modules/nf-core/bcftools/mpileup/main.nf b/modules/nf-core/bcftools/mpileup/main.nf
diff --git a/modules/nf-core/bcftools/mpileup/meta.yml b/modules/nf-core/bcftools/mpileup/meta.yml
diff --git a/modules/nf-core/bcftools/stats/environment.yml b/modules/nf-core/bcftools/stats/environment.yml
diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf
diff --git a/modules/nf-core/bcftools/stats/meta.yml b/modules/nf-core/bcftools/stats/meta.yml
diff --git a/modules/nf-core/bcftools/view/environment.yml b/modules/nf-core/bcftools/view/environment.yml
diff --git a/modules/nf-core/bcftools/view/main.nf b/modules/nf-core/bcftools/view/main.nf
diff --git a/modules/nf-core/bcftools/view/meta.yml b/modules/nf-core/bcftools/view/meta.yml