Merge pull request #179 from atrigila/dev

Fix: use VCF as input in glimpse2

Author: LouisLeNezet

CHANGELOG.md

@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 
 - [#166](https://github.com/nf-core/phaseimpute/pull/166) - Fix depth type to `number` to enable float.
+- [#179](https://github.com/nf-core/phaseimpute/pull/179) - Fix VCF usage in `GLIMPSE2`.
 
 ## v1.0.0 - Black Labrador [2024-12-09]
 

conf/test_vcf.config

@@ -0,0 +1,40 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/phaseimpute -profile test_glimpse2,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '4.GB',
+        time: '1.h'
+    ]
+}
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function with GLIMPSE2'
+
+    // Input data
+    input  = "${projectDir}/tests/csv/sample_vcf.csv"
+
+    // Genome references
+    fasta  = params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz"
+    panel  = "${projectDir}/tests/csv/panel.csv"
+
+    // Pipeline steps
+    steps  = "impute"
+
+    // External params
+    chunks  = "${projectDir}/tests/csv/chunks.csv"
+
+    // Impute tools
+    tools  = "glimpse2"
+}

nextflow.config

@@ -244,6 +244,7 @@ profiles {
     test_panelprep      { includeConfig 'conf/test_panelprep.config'    }
     test_dog            { includeConfig 'conf/test_dog.config'          }
     test_batch          { includeConfig 'conf/test_batch.config'        }
+    test_vcf            { includeConfig 'conf/test_vcf.config'          }
 }
 
 // Load nf-core custom profiles from different Institutions

workflows/phaseimpute/main.nf

@@ -339,7 +339,7 @@ workflow PHASEIMPUTE {
             BAM_IMPUTE_GLIMPSE2(
                 ch_input_bams_withlist
                     .map{ [it[0], it[1], it[2], it[3]] }
-                    .mix(ch_input_type.vcf.combine([])),
+                    .mix(ch_input_type.vcf.combine(Channel.of([[]]))),
                 ch_panel_phased,
                 ch_chunks_glimpse2,
                 ch_fasta