Fix shapeit5 hash divergence

CHANGELOG.md

@@ -50,6 +50,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#281](https://github.com/nf-core/phaseimpute/pull/281) - Fix `diffchr()` function.
 - [#293](https://github.com/nf-core/phaseimpute/pull/293) - Fix nf-core and nextflow linting.
 - [#297](https://github.com/nf-core/phaseimpute/pull/297) - Fix `VCF_NORMALIZE_BCFTOOLS:BCFTOOLS_VIEW` configuration for `remove_samples` to be properly parsed.
+- [#298](https://github.com/nf-core/phaseimpute/pull/298) - Stabilise variants md5 hash when using `VCFLIB_VCFFIXUP` by using `.bcf.gz` files and `.csi` index.
 
 ### `Dependencies`
 

conf/steps/panelprep.config

@@ -22,14 +22,15 @@ process {
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_NORMALIZE_BCFTOOLS:BCFTOOLS_NORM' {
-        ext.args   = ["-m +any", "--output-type z", "--write-index=tbi"].join(' ')
+        ext.args   = ["-m +any", "--output-type b", "--write-index=csi"].join(' ')
         ext.prefix = { "${meta.panel_id}_${meta.chr}_multiallelic" }
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_NORMALIZE_BCFTOOLS:BCFTOOLS_VIEW' {
         ext.args = {
             def rm_samples = params.remove_samples ? "-s^${params.remove_samples}  --force-samples" : ""
-            return "-v snps -m 2 -M 2 --output-type z --write-index=tbi ${rm_samples}"
+            def output_format = params.compute_freq ? "--output-type z" : "--output-type b"
+            return "-v snps -m 2 -M 2 --write-index=csi ${rm_samples} ${output_format}"
         }
         ext.prefix = { "${meta.panel_id}_${meta.chr}_normalized" }
         publishDir = [
@@ -47,21 +48,7 @@ process {
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_NORMALIZE_BCFTOOLS:VCFLIB_VCFFIXUP' {
         ext.prefix = { "${meta.panel_id}_${meta.chr}_fixup" }
-        publishDir = [
-            path: { "${params.outdir}/prep_panel/panel" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename ->
-                if ( !params.phase || params.publish_all ) {
-                    filename
-                } else {
-                    null
-                }
-            }
-        ]
-    }
-
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_NORMALIZE_BCFTOOLS:BCFTOOLS_INDEX' {
-        ext.args   = "--tbi"
+        ext.args2 = "--output-type b --write-index=csi"
         publishDir = [
             path: { "${params.outdir}/prep_panel/panel" },
             mode: params.publish_dir_mode,

modules.json

@@ -203,12 +203,12 @@
                     },
                     "shapeit5/ligate": {
                         "branch": "master",
-                        "git_sha": "25ac0da595fac900aba3041d2bcdd7eb338192d0",
+                        "git_sha": "8556a739676498417d5b323107e8db43089cf303",
                         "installed_by": ["modules", "vcf_phase_shapeit5"]
                     },
                     "shapeit5/phasecommon": {
                         "branch": "master",
-                        "git_sha": "236d7f19efcffccdfac5e1850af2aa035e0de79c",
+                        "git_sha": "8556a739676498417d5b323107e8db43089cf303",
                         "installed_by": ["modules", "vcf_phase_shapeit5"]
                     },
                     "stitch": {
@@ -228,7 +228,7 @@
                     },
                     "vcflib/vcffixup": {
                         "branch": "master",
-                        "git_sha": "9268f2ac9d9c520ffcc8eeb1078b4ccc461697b1",
+                        "git_sha": "ecd5df5f44d895a81bda2b47bc5b760596bce72f",
                         "installed_by": ["modules"]
                     }
                 }