From 9d21a5d851a950372ac1721e4acb0563085dd1f4 Mon Sep 17 00:00:00 2001 From: Louis Date: Tue, 23 Apr 2024 20:44:38 +0200 Subject: [PATCH] Remove merging of individuals for now and add it to road map --- docs/development.md | 2 ++ workflows/phaseimpute/main.nf | 7 +------ 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/docs/development.md b/docs/development.md index 6c4b74a1..c2bd3d19 100644 --- a/docs/development.md +++ b/docs/development.md @@ -17,6 +17,7 @@ - [] Check if panel is necessary depending on the tool selected - [x] Set modules configuration as full path workflow:subworkflow:module - [] Where should the map file go (separate csv or in panel csv) +- [] Add support for imputation by individuals or by groups of individuals ## Run tests @@ -25,6 +26,7 @@ nextflow run main.nf -profile singularity,test --outdir results -resume nextflow run main.nf -profile singularity,test_sim --outdir results -resume nextflow run main.nf -profile singularity,test_validate --outdir results -resume nextflow run main.nf -profile singularity,test_all --outdir results -resume +nextflow run main.nf -profile singularity,test_quilt --outdir results -resume ``` ## Problematic diff --git a/workflows/phaseimpute/main.nf b/workflows/phaseimpute/main.nf index 8f51ddf1..2b653676 100644 --- a/workflows/phaseimpute/main.nf +++ b/workflows/phaseimpute/main.nf @@ -177,13 +177,8 @@ workflow PHASEIMPUTE { // Create chunks from reference VCF MAKE_CHUNKS(ch_panel, ch_fasta) - // Create input QUILT - ch_input_quilt = ch_input_impute - .map { meta, bam, bai -> [["id": "all_samples"] + meta.subMap("chr", "region"), bam, bai] } - .groupTuple () - // Impute BAMs with QUILT - IMPUTE_QUILT(MAKE_CHUNKS.out.ch_hap_legend, ch_input_quilt, MAKE_CHUNKS.out.ch_chunks) + IMPUTE_QUILT(MAKE_CHUNKS.out.ch_hap_legend, ch_input_impute, MAKE_CHUNKS.out.ch_chunks) ch_versions = ch_versions.mix(IMPUTE_QUILT.out.versions) // Add to output channel