Merge pull request #1 from nschcolnicov/update_makegraph

Updated makegraph to makegraph2
EgorGuga · Feb 16, 2024 · 587475d · 587475d
2 parents 29c284f + a12e038
commit 587475d
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Showing 10 changed files with 7 additions and 154 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -25,7 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
-- [#1391](https://github.com/nf-core/sarek/pull/1391) - Fixed input channel for ASSESS_SIGNIFICANCE module, updated makegraph to makegraph2.
+- [#1400](https://github.com/nf-core/sarek/pull/1400) - Fixed input channel for ASSESS_SIGNIFICANCE module, updated makegraph to makegraph2.
 - [#1334](https://github.com/nf-core/sarek/pull/1334) - Remove extra v, when reporting tower runs on slack
 - [#1335](https://github.com/nf-core/sarek/pull/1335) - Add docs and validation for bcftools annotation parameters
 - [#1345](https://github.com/nf-core/sarek/pull/1345) - Preserve STDERR for easier debugging

diff --git a/README.md b/README.md
@@ -151,6 +151,7 @@ We thank the following people for their extensive assistance in the development
 - [Malin Larsson](https://github.com/malinlarsson)
 - [Marcel Martin](https://github.com/marcelm)
 - [Nick Smith](https://github.com/nickhsmith)
+- [Nicolas Schcolnicov](https://github.com/nschcolnicov)
 - [Nilesh Tawari](https://github.com/nilesh-tawari)
 - [Olga Botvinnik](https://github.com/olgabot)
 - [Oskar Wacker](https://github.com/WackerO)

diff --git a/conf/modules/controlfreec.config b/conf/modules/controlfreec.config
@@ -50,7 +50,7 @@ process {
         ]
     }
 
-    withName: 'MAKEGRAPH' {
+    withName: 'MAKEGRAPH2' {
         ext.args   = { "${params.cf_ploidy}" }
         publishDir = [
             mode: params.publish_dir_mode,

diff --git a/modules.json b/modules.json
@@ -107,12 +107,6 @@
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
-                    "controlfreec/makegraph": {
-                        "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff"
-                    },
                     "controlfreec/makegraph2": {
                         "branch": "master",
                         "git_sha": "a7bae48d8bccfae99e3b862fa07bbd50a8df6b82",

diff --git a/modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff b/modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff
diff --git a/modules/nf-core/controlfreec/makegraph/environment.yml b/modules/nf-core/controlfreec/makegraph/environment.yml
diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf
diff --git a/modules/nf-core/controlfreec/makegraph/meta.yml b/modules/nf-core/controlfreec/makegraph/meta.yml
diff --git a/subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf b/subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf
@@ -8,7 +8,7 @@ include { CONTROLFREEC_FREEC as FREEC_TUMORONLY                  } from '../../.
 include { CONTROLFREEC_ASSESSSIGNIFICANCE as ASSESS_SIGNIFICANCE } from '../../../modules/nf-core/controlfreec/assesssignificance/main'
 include { CONTROLFREEC_FREEC2BED as FREEC2BED                    } from '../../../modules/nf-core/controlfreec/freec2bed/main'
 include { CONTROLFREEC_FREEC2CIRCOS as FREEC2CIRCOS              } from '../../../modules/nf-core/controlfreec/freec2circos/main'
-include { CONTROLFREEC_MAKEGRAPH as MAKEGRAPH                    } from '../../../modules/nf-core/controlfreec/makegraph/main'
+include { CONTROLFREEC_MAKEGRAPH2 as MAKEGRAPH2                  } from '../../../modules/nf-core/controlfreec/makegraph2/main'
 
 workflow BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC {
     take:
@@ -30,13 +30,13 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC {
     ASSESS_SIGNIFICANCE(FREEC_TUMORONLY.out.CNV.join(FREEC_TUMORONLY.out.ratio, failOnDuplicate: true, failOnMismatch: true))
     FREEC2BED(FREEC_TUMORONLY.out.ratio)
     FREEC2CIRCOS(FREEC_TUMORONLY.out.ratio)
-    MAKEGRAPH(FREEC_TUMORONLY.out.ratio.join(FREEC_TUMORONLY.out.BAF, failOnDuplicate: true, failOnMismatch: true))
+    MAKEGRAPH2(FREEC_TUMORONLY.out.ratio.join(FREEC_TUMORONLY.out.BAF, failOnDuplicate: true, failOnMismatch: true))
 
     ch_versions = ch_versions.mix(FREEC_TUMORONLY.out.versions)
     ch_versions = ch_versions.mix(ASSESS_SIGNIFICANCE.out.versions)
     ch_versions = ch_versions.mix(FREEC2BED.out.versions)
     ch_versions = ch_versions.mix(FREEC2CIRCOS.out.versions)
-    ch_versions = ch_versions.mix(MAKEGRAPH.out.versions)
+    ch_versions = ch_versions.mix(MAKEGRAPH2.out.versions)
 
     emit:
     versions = ch_versions

diff --git a/tests/config/pytesttags.yml b/tests/config/pytesttags.yml
@@ -248,7 +248,7 @@ controlfreec:
   - modules/nf-core/controlfreec/freec/**
   - modules/nf-core/controlfreec/freec2bed/**
   - modules/nf-core/controlfreec/freec2circos/**
-  - modules/nf-core/controlfreec/makegraph/**
+  - modules/nf-core/controlfreec/makegraph2/**
   - modules/nf-core/samtools/mpileup/**
   - subworkflows/local/bam_variant_calling_mpileup/**
   - subworkflows/local/bam_variant_calling_somatic_all/**