From 7d78d9f3b02e0e8da6d456055ed33739cf8df556 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 29 Jan 2024 16:25:48 +0100
Subject: [PATCH] fix linting

---
 .../local/germlinecnvcaller_cohort.nf         | 50 +++++++++----------
 workflows/createpanelrefs.nf                  |  8 +--
 2 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/subworkflows/local/germlinecnvcaller_cohort.nf b/subworkflows/local/germlinecnvcaller_cohort.nf
index 4e1b9ef..606f835 100644
--- a/subworkflows/local/germlinecnvcaller_cohort.nf
+++ b/subworkflows/local/germlinecnvcaller_cohort.nf
@@ -23,9 +23,9 @@ workflow GERMLINECNVCALLER_COHORT {
         //
         //  Prepare references
         //
-        SAMTOOLS_FAIDX (ch_fasta, [[:],[]])
+        SAMTOOLS_FAIDX(ch_fasta, [[:],[]])
 
-        PICARD_CREATESEQUENCEDICTIONARY (ch_fasta)
+        PICARD_CREATESEQUENCEDICTIONARY(ch_fasta)
 
         ch_user_dict
             .mix(PICARD_CREATESEQUENCEDICTIONARY.out.reference_dict)
@@ -37,16 +37,16 @@ workflow GERMLINECNVCALLER_COHORT {
             .collect()
             .set { ch_fai }
 
-        GATK4_PREPROCESSINTERVALS (ch_fasta,
-                                   ch_fai,
-                                   ch_dict,
-                                   [[:],[]], [[:],[]])
+        GATK4_PREPROCESSINTERVALS(ch_fasta,
+                                ch_fai,
+                                ch_dict,
+                                [[:],[]], [[:],[]])
 
-        GATK4_ANNOTATEINTERVALS (GATK4_PREPROCESSINTERVALS.out.interval_list,
-                                 ch_fasta,
-                                 ch_fai,
-                                 ch_dict,
-                                 [[:],[]], [[:],[]], [[:],[]], [[:],[]])
+        GATK4_ANNOTATEINTERVALS(GATK4_PREPROCESSINTERVALS.out.interval_list,
+                                ch_fasta,
+                                ch_fai,
+                                ch_dict,
+                                [[:],[]], [[:],[]], [[:],[]], [[:],[]])
 
         //
         // Filter out files that lack indices, and generate them
@@ -60,11 +60,11 @@ workflow GERMLINECNVCALLER_COHORT {
                 }
                 .set { ch_for_mix }
 
-        SAMTOOLS_INDEX (ch_for_mix.alignment_without_index)
+        SAMTOOLS_INDEX(ch_for_mix.alignment_without_index)
 
         SAMTOOLS_INDEX.out.bai
-               .mix(SAMTOOLS_INDEX.out.crai)
-               .set { ch_index }
+            .mix(SAMTOOLS_INDEX.out.crai)
+            .set { ch_index }
 
         //
         // Collect alignment files and their indices
@@ -78,10 +78,10 @@ workflow GERMLINECNVCALLER_COHORT {
         //
         // Collect read counts, and generate models
         //
-        GATK4_COLLECTREADCOUNTS (ch_readcounts_in,
-                                 ch_fasta,
-                                 ch_fai,
-                                 ch_dict)
+        GATK4_COLLECTREADCOUNTS(ch_readcounts_in,
+                                ch_fasta,
+                                ch_fai,
+                                ch_dict)
 
         GATK4_COLLECTREADCOUNTS.out.tsv
                                 .mix(GATK4_COLLECTREADCOUNTS.out.hdf5)
@@ -90,9 +90,9 @@ workflow GERMLINECNVCALLER_COHORT {
                                 .set { ch_readcounts_out }
 
 
-        GATK4_FILTERINTERVALS (GATK4_PREPROCESSINTERVALS.out.interval_list,
-                               ch_readcounts_out,
-                               GATK4_ANNOTATEINTERVALS.out.annotated_intervals)
+        GATK4_FILTERINTERVALS(GATK4_PREPROCESSINTERVALS.out.interval_list,
+                            ch_readcounts_out,
+                            GATK4_ANNOTATEINTERVALS.out.annotated_intervals)
 
         GATK4_INTERVALLISTTOOLS(GATK4_FILTERINTERVALS.out.interval_list)
                                 .interval_list
@@ -105,9 +105,9 @@ workflow GERMLINECNVCALLER_COHORT {
                 .map{ meta, counts, meta2, il -> [meta, counts, il, []] }
                 .set {ch_contigploidy_in}
 
-        GATK4_DETERMINEGERMLINECONTIGPLOIDY (ch_contigploidy_in,
-                                             [[:],[]],
-                                             ch_ploidy_priors)
+        GATK4_DETERMINEGERMLINECONTIGPLOIDY(ch_contigploidy_in,
+                                            [[:],[]],
+                                            ch_ploidy_priors)
 
         ch_readcounts_out
                 .combine(ch_intervallist_out)
@@ -115,7 +115,7 @@ workflow GERMLINECNVCALLER_COHORT {
                 .map{ meta, counts, il, meta2, calls -> [meta + [id:il.baseName],  counts, il, calls, []] }
                 .set {ch_cnvcaller_in}
 
-        GATK4_GERMLINECNVCALLER (ch_cnvcaller_in)
+        GATK4_GERMLINECNVCALLER(ch_cnvcaller_in)
 
         ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
         ch_versions = ch_versions.mix(PICARD_CREATESEQUENCEDICTIONARY.out.versions)
diff --git a/workflows/createpanelrefs.nf b/workflows/createpanelrefs.nf
index 478da79..b2b6c4d 100644
--- a/workflows/createpanelrefs.nf
+++ b/workflows/createpanelrefs.nf
@@ -126,10 +126,10 @@ workflow CREATEPANELREFS {
     if (params.tools && params.tools.split(',').contains('germlinecnvcaller')) {
 
         GERMLINECNVCALLER_COHORT(ch_dict,
-                                 ch_fai,
-                                 ch_fasta,
-                                 ch_input,
-                                 ch_ploidy_priors)
+                                ch_fai,
+                                ch_fasta,
+                                ch_input,
+                                ch_ploidy_priors)
 
         ch_versions = ch_versions.mix(GERMLINECNVCALLER_COHORT.out.versions)
     }