Merge pull request nf-core#51 from LouisLeNezet/update

Update modules and fix linting

.nf-core.yml

@@ -1,2 +1,4 @@
 repository_type: pipeline
+lint:
+  subworkflow_changes: false
 nf_core_version: "2.14.1"

CHANGELOG.md

@@ -9,6 +9,10 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co
 
 ### `Added`
 
+- [#20](https://github.com/nf-core/phaseimpute/pull/20) - Added automatic detection of vcf contigs for the reference panel and automatic renaming available
+- [#22](https://github.com/nf-core/phaseimpute/pull/20) - Add validation step for concordance analysis. Input channels changed to match inputs steps. Outdir folder organised by steps. Modules config by subworkflows.
+- [#26](https://github.com/nf-core/phaseimpute/pull/26) - Added QUILT method
+
 ### `Changed`
 
 - [#18](https://github.com/nf-core/phaseimpute/pull/18)
@@ -17,9 +21,7 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co
   - correct meta map propagation
   - Test impute and test sim works
 - [#19](https://github.com/nf-core/phaseimpute/pull/19) - Changed reference panel to accept a csv, update modules and subworkflows (glimpse1/2 and shapeit5)
-- [#20](https://github.com/nf-core/phaseimpute/pull/20) - Added automatic detection of vcf contigs for the reference panel and automatic renaming available
-- [#22](https://github.com/nf-core/phaseimpute/pull/20) - Add validation step for concordance analysis. Input channels changed to match inputs steps. Outdir folder organised by steps. Modules config by subworkflows.
-- [#26](https://github.com/nf-core/phaseimpute/pull/26) - Added QUILT method
+- [#51](https://github.com/nf-core/phaseimpute/pull/51) - Update all process and fix linting errors. Remove fastqc added by the template.
 
 ### `Fixed`
 

modules.json

@@ -7,13 +7,13 @@
                 "nf-core": {
                     "bcftools/annotate": {
                         "branch": "master",
-                        "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
+                        "git_sha": "2ad29c2aed06d815d9f68ad7ba20b3b1c574ce9c",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff"
                     },
                     "bcftools/concat": {
                         "branch": "master",
-                        "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
+                        "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/bcftools/concat/bcftools-concat.diff"
                     },
@@ -25,16 +25,11 @@
                     "bcftools/index": {
                         "branch": "master",
                         "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
-                        "installed_by": [
-                            "modules",
-                            "multiple_impute_glimpse2",
-                            "vcf_impute_glimpse",
-                            "vcf_phase_shapeit5"
-                        ]
+                        "installed_by": ["multiple_impute_glimpse2", "vcf_impute_glimpse", "vcf_phase_shapeit5"]
                     },
                     "bcftools/mpileup": {
                         "branch": "master",
-                        "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
+                        "git_sha": "e7df38a545d7d72083eededabd8849f731a01502",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/bcftools/mpileup/bcftools-mpileup.diff"
                     },
@@ -64,14 +59,9 @@
                         "git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1",
                         "installed_by": ["modules"]
                     },
-                    "fastqc": {
-                        "branch": "master",
-                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
-                        "installed_by": ["modules"]
-                    },
                     "gawk": {
                         "branch": "master",
-                        "git_sha": "da4d05d04e65227d4307e87940842f1a14de62c7",
+                        "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
                         "installed_by": ["modules"]
                     },
                     "glimpse/chunk": {
@@ -101,7 +91,7 @@
                     },
                     "glimpse2/ligate": {
                         "branch": "master",
-                        "git_sha": "ee7fee68281944b002bd27a8ff3f19200b4d3fad",
+                        "git_sha": "09d793219114004f268b98663b12f8062097a8c5",
                         "installed_by": ["multiple_impute_glimpse2"]
                     },
                     "glimpse2/phase": {
@@ -205,6 +195,11 @@
                         "branch": "master",
                         "git_sha": "7e56daae390ff896b292ddc70823447683a79936",
                         "installed_by": ["subworkflows"]
+                    },
+                    "vcf_phase_shapeit5": {
+                        "branch": "master",
+                        "git_sha": "dcf17cc0ed8fd5ea57e61a13e0147cddb5c1ee30",
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }