Conda check removed and seed parameters added for QUILT (#146)

* Remove conda from PR test

* Add seed for stitch and quilt

* Bump version in nf-core yml

* Update changelog

Author: LouisLeNezet

.github/workflows/ci.yml

@@ -40,7 +40,6 @@ jobs:
           - "24.04.2"
           - "latest-everything"
         profile:
-          - "conda"
           - "docker"
           - "singularity"
         TEST_PROFILE:

.nf-core.yml

@@ -1,6 +1,4 @@
 bump_version: null
-lint:
-  subworkflow_changes: false
 nf_core_version: 3.0.2
 org_path: null
 repository_type: pipeline
@@ -13,5 +11,5 @@ template:
   org: nf-core
   outdir: .
   skip_features: null
-  version: 1.0dev
+  version: 1.0.0
 update: null

CHANGELOG.md

@@ -23,6 +23,7 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co
 - [#111](https://github.com/nf-core/phaseimpute/pull/111) - Add nf-test for all sbwf, wf, modules and functions.
 - [#131](https://github.com/nf-core/phaseimpute/pull/131) - Set normalisation as optional. Fix extension detection function. Add support for validation with vcf files. Concatenate vcf only if more than one file. Change `--phased` to `--phase` for consistency.
 - [#143](https://github.com/nf-core/phaseimpute/pull/143) - Improve contigs warning and error logging. The number of chromosomes contigs is summarized if above `max_chr_names`.
+- [#146](https://github.com/nf-core/phaseimpute/pull/146) - Add `seed` parameter for `QUILT`
 
 ### `Changed`
 
@@ -58,6 +59,7 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co
 - [#103](https://github.com/nf-core/phaseimpute/pull/103) - Update Glimpse2 phase, gunzip and multiqc
 - [#135](https://github.com/nf-core/phaseimpute/pull/135) - Impute by batch of 100 individuals by default using `--batch_size` parameter. All individuals BAM files are gathered and VCF are allowed for glimpse1 and glimpse2. Channel preprocessing of stitch is done in stitch subworkflow. Genotype likelihood computation for glimpse1 is now done outside of the subworkflow and merge the resulting vcf with all the samples. New test added to check batch separation. Improve `usage.md` documentation. Add validation to initialisation of the pipeline to ensure compatibility between tools, steps and the files provided by the user.
 - [#139](https://github.com/nf-core/phaseimpute/pull/139) - Update all nf-core modules
+- [#146](https://github.com/nf-core/phaseimpute/pull/146) - Remove conda CI check for PR due to nextflow error
 
 ### `Fixed`
 

conf/steps/imputation_quilt.config

@@ -22,6 +22,7 @@ process {
 
     // Impute quilt
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_QUILT:QUILT_QUILT' {
+        ext.args = "--seed=${params.seed}"
         ext.prefix = { "${meta.id}_batch${meta.batch}_${meta.chr}_${meta.chunk}.impute" }
         publishDir = [enabled: false]
     }

nextflow_schema.json

@@ -154,6 +154,12 @@
                     "mimetype": "text/csv",
                     "schema": "/assets/schema_chunks.json",
                     "pattern": "^\\S+\\.csv$"
+                },
+                "seed": {
+                    "type": "integer",
+                    "description": "Seed for random number generation in Stitch and Quilt software",
+                    "hidden": true,
+                    "default": 1
                 }
             }
         },
@@ -426,10 +432,6 @@
             "description": "Arguments to customize STITCH run",
             "default": "",
             "properties": {
-                "seed": {
-                    "type": "integer",
-                    "default": 1
-                },
                 "posfile": {
                     "type": "string",
                     "description": "Path to comma-separated file containing tab-separated files describing the variable positions to be used for imputation. Refer to the documentation for the `--posfile` argument of STITCH for more information.",