picard/collecthsmetrics fails for gzipped genomes

[znorgaard]

Have you checked the docs?

• [x] nf-core website: troubleshooting
• [x] nf-core modules documentation

Description of the bug

picard CollectHsMetrics requires a .gzi file when running on a gzipped fasta. This is not currently an input option for the process.

You'll get an error in the process that looks like:

Exception in thread "main" java.lang.UnsupportedOperationException: Index does not appear to exist for GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18.fasta.gz.  samtools faidx can be used to create an index

Adding an input of the .gzi file (which is also output by samtools faidx when run on a fasta.gz) resolves this problem.

Command used and terminal output

Relevant files

No response

System information

No response