This pull request adds support for samplesheet input integration instead of --input /path/to/fastqs/"*_{1,2}.fq.gz" that was previously supported. This now allows easier testing with test datasets in a samplesheet in a github repo and clarity for which samples were ran when launching on Tower.
Other commits are small fixes to the organization and commenting of the workflow script. In the check_samplesheet.py script there are 3 lines of code commented out that check for a header in the samplesheet that throw an error even when there is a header, such as when supplying nf-core samplesheets containing a header and the correct column names the workflow expects.
Many of these things were probably supported at some point when the workflow was created with nf-core create but I pulled them out when experimenting with them during a time when I didn't quite know what I was doing, so most of this is putting nf-core things back in. CI tests don't quite work yet, that is next on my to-do list.
This pull request adds support for samplesheet input integration instead of
--input /path/to/fastqs/"*_{1,2}.fq.gz"that was previously supported. This now allows easier testing with test datasets in a samplesheet in a github repo and clarity for which samples were ran when launching on Tower.Other commits are small fixes to the organization and commenting of the workflow script. In the
check_samplesheet.pyscript there are 3 lines of code commented out that check for a header in the samplesheet that throw an error even when there is a header, such as when supplying nf-core samplesheets containing a header and the correct column names the workflow expects.Many of these things were probably supported at some point when the workflow was created with
nf-core createbut I pulled them out when experimenting with them during a time when I didn't quite know what I was doing, so most of this is puttingnf-corethings back in. CI tests don't quite work yet, that is next on my to-do list.