From 0fafaeebf52cc5ab554b83297ed02a48d852a848 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 13 Dec 2021 16:15:20 +0000 Subject: [PATCH] Revert PR #1147 (#1166) * Revert PR #1147 * Fix md5sum for crai file --- modules/samtools/index/main.nf | 11 ++++------- tests/modules/samtools/index/test.yml | 2 +- 2 files changed, 5 insertions(+), 8 deletions(-) diff --git a/modules/samtools/index/main.nf b/modules/samtools/index/main.nf index 74ae15df..db025a8f 100644 --- a/modules/samtools/index/main.nf +++ b/modules/samtools/index/main.nf @@ -11,13 +11,10 @@ process SAMTOOLS_INDEX { tuple val(meta), path(input) output: - tuple val(meta), path("*.bam" , includeInputs:true), path("*.bai") , optional:true, emit: bam_bai - tuple val(meta), path("*.bai") , optional:true, emit: bai - tuple val(meta), path("*.bam" , includeInputs:true), path("*.csi") , optional:true, emit: bam_csi - tuple val(meta), path("*.csi") , optional:true, emit: csi - tuple val(meta), path("*.cram", includeInputs:true), path("*.crai"), optional:true, emit: cram_crai - tuple val(meta), path("*.crai") , optional:true, emit: crai - path "versions.yml" , emit: versions + tuple val(meta), path("*.bai") , optional:true, emit: bai + tuple val(meta), path("*.csi") , optional:true, emit: csi + tuple val(meta), path("*.crai"), optional:true, emit: crai + path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' diff --git a/tests/modules/samtools/index/test.yml b/tests/modules/samtools/index/test.yml index 6972ed65..7184be8f 100644 --- a/tests/modules/samtools/index/test.yml +++ b/tests/modules/samtools/index/test.yml @@ -14,7 +14,7 @@ - samtools/index files: - path: output/samtools/test.paired_end.recalibrated.sorted.cram.crai - md5sum: 537e3d8c937bcc4e34e1cf47cd71d484 + md5sum: 14bc3bd5c89cacc8f4541f9062429029 - name: samtools index test_samtools_index_csi command: nextflow run ./tests/modules/samtools/index -entry test_samtools_index_csi -c ./tests/config/nextflow.config -c ./tests/modules/samtools/index/nextflow.config