diff --git a/modules/bclconvert/main.nf b/modules/bclconvert/main.nf index c891ab7f..7c32bd6f 100644 --- a/modules/bclconvert/main.nf +++ b/modules/bclconvert/main.nf @@ -5,7 +5,7 @@ process BCLCONVERT { if (params.enable_conda) { exit 1, "Conda environments cannot be used when using bcl-convert. Please use docker or singularity containers." } - container "nfcore/bclconvert:3.9.3" + container "nfcore/bclconvert:3.10.5" input: tuple val(meta), path(samplesheet), path(run_dir) @@ -13,7 +13,7 @@ process BCLCONVERT { output: tuple val(meta), path("**[!Undetermined]_S*_L00?_R?_00?.fastq.gz") ,emit: fastq tuple val(meta), path("**_S*_L00?_I?_00?.fastq.gz") ,optional:true ,emit: fastq_idx - tuple val(meta), path("Undetermined_S0_L00?_R?_00?.fastq.gz") ,emit: undetermined + tuple val(meta), path("Undetermined_S0_L00?_R?_00?.fastq.gz") ,optional:true ,emit: undetermined tuple val(meta), path("Undetermined_S0_L00?_I?_00?.fastq.gz") ,optional:true, emit: undetermined_idx tuple val(meta), path("Reports") ,emit: reports tuple val(meta), path("Logs") ,emit: logs diff --git a/modules/bclconvert/meta.yml b/modules/bclconvert/meta.yml index 91d2ca6a..82ebf0fe 100644 --- a/modules/bclconvert/meta.yml +++ b/modules/bclconvert/meta.yml @@ -39,7 +39,7 @@ output: pattern: "**_S*_L00?_I?_00?.fastq.gz" - undetermined: type: file - description: Undetermined sample FASTQ files + description: Optional undetermined sample FASTQ files pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz" - undetermined_idx: type: file diff --git a/tests/modules/bclconvert/test.yml b/tests/modules/bclconvert/test.yml index f03b72e2..74aab696 100644 --- a/tests/modules/bclconvert/test.yml +++ b/tests/modules/bclconvert/test.yml @@ -10,7 +10,7 @@ - path: output/bclconvert/Reports/Adapter_Metrics.csv md5sum: 989240b8840b2169ac1061f952c90f6c - path: output/bclconvert/Reports/Demultiplex_Stats.csv - md5sum: bb2ed9c6b46e03fbc060efd2c75398b0 + md5sum: 93949a8cd96f907d83e0808c1ec2a04b - path: output/bclconvert/Reports/IndexMetricsOut.bin md5sum: 9e688c58a5487b8eaf69c9e1005ad0bf - path: output/bclconvert/Reports/Index_Hopping_Counts.csv @@ -26,7 +26,7 @@ - path: output/bclconvert/Reports/fastq_list.csv md5sum: 05bc84f51840f5754cfb8381b36f2cb0 - path: output/bclconvert/Sample1_S1_L001_R1_001.fastq.gz - md5sum: 883037281293a2ec4995d34257f19866 + md5sum: 57d2f3b389656245f923351d3e3d2d65 - path: output/bclconvert/Undetermined_S0_L001_R1_001.fastq.gz md5sum: a4745abc5e7fdb89cc6df3069f3c6e69 - path: output/bclconvert/flowcell/InterOp/ControlMetricsOut.bin