diff --git a/modules/samtools/stats/main.nf b/modules/samtools/stats/main.nf index c913bc5e..89b92d79 100644 --- a/modules/samtools/stats/main.nf +++ b/modules/samtools/stats/main.nf @@ -8,7 +8,7 @@ process SAMTOOLS_STATS { 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" input: - tuple val(meta), path(bam), path(bai) + tuple val(meta), path(input), path(input_index) path fasta output: @@ -27,7 +27,7 @@ process SAMTOOLS_STATS { stats \\ --threads ${task.cpus-1} \\ ${reference} \\ - ${bam} \\ + ${input} \\ > ${prefix}.stats cat <<-END_VERSIONS > versions.yml