From 3c75649e8596b9a1bb56caac1b8d889e7ddcc8c8 Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmaio.com>
Date: Wed, 13 Nov 2024 16:56:48 +0100
Subject: [PATCH] Update changelog and remove bcftools query from config

---
 CHANGELOG.md                                               | 2 +-
 conf/modules.config                                        | 7 -------
 .../local/vcf_split_bcftools/tests/nextflow.config         | 4 ----
 3 files changed, 1 insertion(+), 12 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 95905392..7a26f9b7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -74,7 +74,7 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu) and [Mazza
 - [#117](https://github.com/nf-core/phaseimpute/pull/117) - Fix directories in CSV.
 - [#151](https://github.com/nf-core/phaseimpute/pull/151) - Fix `Type not supported: class org.codehaus.groovy.runtime.GStringImpl` error due to `String` test in `getFileExtension()`.
 - [#153](https://github.com/nf-core/phaseimpute/pull/153) - Fix getFileExtension function. Fix image in `usage.md`. Fix small warnings and errors with updated language server. `def` has been added when necessary, `:` use instead of `,` in assertions, `_` added to variables not used in closures, `for` loop replaced by `.each{}`, remove unused code / input.
-- [#158](https://github.com/nf-core/phaseimpute/pull/158) - Fix contigs usage when regions is only a subset of the given contigs (e.g. if panel file has the 22 chr and the region file only 2 then only the 2 common will be processed). Fix `VCF_SPLIT_BCFTOOLS` by checking first if there is at least one sample and only if more than one then proceed with splitting.
+- [#158](https://github.com/nf-core/phaseimpute/pull/158) - Fix contigs usage when regions is only a subset of the given contigs (e.g. if panel file has the 22 chr and the region file only 2 then only the 2 common will be processed). Fix `multiQC` samples names for better comprehension. Fix `-resume` errors when `ch_fasta` is use by adding `cache = 'lenient'` in necessary processes. Fix `BCFTOOLS_PLUGINSPLIT` in edge case with only one sample. Fix `--window-size` of `GLIMPSE_CHUNK` from `4` to `4000000`.
 
 ### `Dependencies`
 
diff --git a/conf/modules.config b/conf/modules.config
index 8c92345c..a9827d8d 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -87,13 +87,6 @@ process {
     }
 
     // Split by samples for each tool
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_SPLIT_BCFTOOLS:BCFTOOLS_QUERY' {
-        tag = { "${meta.id} Batch ${meta.batch} ${meta.tools}" }
-        ext.args = "--list-samples"
-        ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.tools}" }
-        publishDir = [enabled: false]
-    }
-
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_SPLIT_BCFTOOLS:BCFTOOLS_PLUGINSPLIT' {
         tag = { "${meta.id} Batch ${meta.batch} ${meta.tools}" }
         ext.args   = ["--output-type z", "--write-index=tbi"].join(' ')
diff --git a/subworkflows/local/vcf_split_bcftools/tests/nextflow.config b/subworkflows/local/vcf_split_bcftools/tests/nextflow.config
index 350757c2..a2282fbf 100644
--- a/subworkflows/local/vcf_split_bcftools/tests/nextflow.config
+++ b/subworkflows/local/vcf_split_bcftools/tests/nextflow.config
@@ -5,10 +5,6 @@ process {
         ext.args = ["--write-index=tbi", "--output-type z"].join(' ')
     }
 
-    withName: BCFTOOLS_QUERY {
-        ext.args = "--list-samples"
-    }
-
     withName: BCFTOOLS_PLUGINSPLIT {
         ext.args = ["--write-index=tbi", "--output-type z"].join(' ')
     }