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Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com>
Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com>
Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com>
| def args = task.ext.args ?: '' | ||
| def args2 = task.ext.args2 ?: '' // args2 is used to specify a program when no program file has been given | ||
| program = program_file ? "-f ${program_file}" : "${args2}" | ||
| awk_ext = bioawk_extension ? "-c ${bioawk_extension}" : "" |
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This can just be supplied in ext.args
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Can you add a test for the program file? |
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Looks good, but still an open question about supplying the -c option in args
| def args = task.ext.args ?: '' | ||
| def args2 = task.ext.args2 ?: '' // args2 is used to specify a program when no program file has been given | ||
| program = program_file ? "-f ${program_file}" : "${args2}" | ||
| awk_ext = bioawk_extension ? "-c ${bioawk_extension}" : "" |
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Update bioawk to be closer to gawk, mainly so it can take a program file
Linked to: sanger-tol/nf-core-modules#216
EDIT: I ended up in an odd merge conflict situation where the previous PR's commits were included