Update glimpse2_phase gunzip & multiqc (#103)

* Update glimpse2 phase to nf-core

* Update gunzip

* Update multiqc

* Update changelog

* remove unused subworkflow (#105)

* Fix chr name errors (#102)

* Compute chr list from vcf not from whole file

* Update all nf-core modules (#100)

* Update Bcftools annotate

* Update Bcftools concat

* Update Bcftools convert

* Update Bcftools index

* Update Bcftools norm

* Update bcftools pluginsplit

* Remove unused bcftools query

* Update bcftools view

* Update dumpsoftwareversions

* Update Gawk

* Update glimpse2 chunk

* Update glimpse2 concordance

* Update glimpse2 ligate splitreference

* Update glimpse2 phase

* Update Gunzip

* Update multiqc

* Update samtools faidx

* Update samtools merge

* Update samtools index

* Update samtools reheader

* Update samtools view

* Update modules.json

* Patch samtools view

* Update bcftools

* Patch bcftools concat

* Fix getfilesextension for null file, add debug and fix variable

* Update gawk

* Fix samtools index

* Update changelog

* Remove uncessary process

* Fix chunking

* Update snapshot

* Update snapshot

* Update snapshot

* Update checkFileIndex function to collect the file before checking

---------

Co-authored-by: LouisLeNezet <[email protected]>

* Update getFileExtension

* Fix checkFileIndex

* Set ch_regions as intersect of contigs, add test and documentation

* Add more comment

* Add test for checkFileIndex

* remove unused subworkflow (#105)

* Update data tests sets

* Update Quilt sbwf, fix checkFileIndex, update snapshot

* Update snapshot and function test

* Add dog test

* Update subworkflows/local/utils_nfcore_phaseimpute_pipeline/tests/function.nf.test

Co-authored-by: Anabella Trigila <[email protected]>

* Add more test to vcf_chr_rename

---------

Co-authored-by: LouisLeNezet <[email protected]>
Co-authored-by: Anabella Trigila <[email protected]>

---------

Co-authored-by: LouisLeNezet <[email protected]>
Co-authored-by: Anabella Trigila <[email protected]>

CHANGELOG.md

@@ -50,6 +50,7 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co
 - [#102](https://github.com/nf-core/phaseimpute/pull/102) - Compute chr name from whole vcf.
 - [#102](https://github.com/nf-core/phaseimpute/pull/102) - Only warn the user if some contigs are absent from files, the regions to compute is now the intersection of regions, panel, posfile, chunks, map.
 - [#102](https://github.com/nf-core/phaseimpute/pull/102) - Update all test and recompute snapshot to match new version of the phaseimpute test dataset.
+- [#103](https://github.com/nf-core/phaseimpute/pull/103) - Update Glimpse2 phase, gunzip and multiqc
 
 ### `Fixed`
 

modules.json

@@ -25,7 +25,7 @@
                     "bcftools/index": {
                         "branch": "master",
                         "git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f",
-                        "installed_by": ["bam_impute_glimpse", "multiple_impute_glimpse2", "vcf_phase_shapeit5"]
+                        "installed_by": ["bam_impute_glimpse", "vcf_phase_shapeit5"]
                     },
                     "bcftools/mpileup": {
                         "branch": "master",
@@ -88,7 +88,7 @@
                     "glimpse2/chunk": {
                         "branch": "master",
                         "git_sha": "d735292b38270792799d18d3b4948ea4f815b5a7",
-                        "installed_by": ["multiple_impute_glimpse2"],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/glimpse2/chunk/glimpse2-chunk.diff"
                     },
                     "glimpse2/concordance": {
@@ -99,27 +99,26 @@
                     "glimpse2/ligate": {
                         "branch": "master",
                         "git_sha": "d735292b38270792799d18d3b4948ea4f815b5a7",
-                        "installed_by": ["multiple_impute_glimpse2"]
+                        "installed_by": ["modules"]
                     },
                     "glimpse2/phase": {
                         "branch": "master",
-                        "git_sha": "d735292b38270792799d18d3b4948ea4f815b5a7",
-                        "installed_by": ["multiple_impute_glimpse2"],
-                        "patch": "modules/nf-core/glimpse2/phase/glimpse2-phase.diff"
+                        "git_sha": "6a5a6e1dedc88826744e8117c1974dcca4829d8f",
+                        "installed_by": ["modules"]
                     },
                     "glimpse2/splitreference": {
                         "branch": "master",
                         "git_sha": "d735292b38270792799d18d3b4948ea4f815b5a7",
-                        "installed_by": ["multiple_impute_glimpse2"]
+                        "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "a7231cbccb86535529e33859e05d19ac93f3ea04",
+                        "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "45d482f013f7da8a3e050e855f04ada418d91c3c",
+                        "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
                         "installed_by": ["modules"]
                     },
                     "quilt/quilt": {