Help to resolve error: input files are not included in the default matching set

[Ravneet Kaur]

Dear Members,

I am creating my first DSL2 pipeline. But got stuck with an error. I am wondering if someone knows how to resolve the issue.

My DSL2 workflow is as below:

It is running fine until the BWAMEM2_MEM (CUTADAPT.out.reads, BWAMEM2_INDEX.out.index) step.

After this above step, I am using a subworkflow: BAM_SORT_SAMTOOLS, the details of which can be seen below:

But this subworkflow is giving the following error:

The input file (test278.bam) is included in the command as it can be seen in the above picture. Then why this error is appearing? If anyone can give any suggestions.

Many thanks for you time.

Rav

[Ravneet Kaur]

Dear Members,

The issue is resolved: The input and the output files for the SAMTOOLS_SORT module had same names. After changing the name of the output file, the issue is resolved.

Many thanks,

Rav

signature   Ravneet

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