Do not resolve paths for bamfile and barcodes:

[tucano]

In nextflow files are staged with soft links in a working directory.

If you follow soft links you end up searching for cellsorted_ file in the input directory not in the working directory.

Consider this small example:

lrwxrwxrwx 1 davide.rambaldi sottoriva   36 May  8 16:41 barcodes.tsv.gz -> ../testdata/Sample_X/barcodes.tsv.gz
-rw-r--r-- 1 davide.rambaldi sottoriva 7.0M May  8 16:56 cellsorted_possorted_genome_bam.bam
lrwxrwxrwx 1 davide.rambaldi sottoriva   45 May  8 16:41 possorted_genome_bam.bam -> ../testdata/Sample_X/possorted_genome_bam.bam
lrwxrwxrwx 1 davide.rambaldi sottoriva   49 May  8 16:41 possorted_genome_bam.bam.bai -> ../testdata/Sample_X/possorted_genome_bam.bam.bai
-rw-r--r-- 1 davide.rambaldi sottoriva 1.2M May  8 16:56 Sample_X_T1.loom

If you resolve paths in this directory (an example working dir from nextflow with soft links) you end up creating ellsorted_possorted_genome_bam.bam file outside the working directoru in the original input dir and the pipeline, that looks for a cellsorted file in the working dir, will fail.

Best Regards.

Davide Rambaldi (Human Technopole)

With this fix we are able to call velocyto in a nextflow pipeline