Hello again, We had fieldbioinformatics in salsa but not on the excel table or the distribution. Luckily it was an easy package.
I merged my d/control a bit with what I found on salsa. What I have not done but feel much tempted to do is to rename the fieldbioinformatics binary to python3-artic. I could also imagine to have a "Provides: fieldbioinformatics" line. The reason is that artic is the python module and the Debian convention is to then provide such a package. It is also the name that conda has chosen, and the package is referenced as artic many times (https://anaconda.org/bioconda/artic). Opinions? Best, Steffen drwxr-xr-x root/root 0 2020-06-27 20:45 ./ drwxr-xr-x root/root 0 2020-06-27 20:45 ./usr/ drwxr-xr-x root/root 0 2020-06-27 20:45 ./usr/bin/ -rwxr-xr-x root/root 382 2020-06-27 20:45 ./usr/bin/align_trim -rwxr-xr-x root/root 386 2020-06-27 20:45 ./usr/bin/align_trim_n -rwxr-xr-x root/root 372 2020-06-27 20:45 ./usr/bin/artic -rwxr-xr-x root/root 398 2020-06-27 20:45 ./usr/bin/artic_fasta_header -rwxr-xr-x root/root 404 2020-06-27 20:45 ./usr/bin/artic_make_depth_mask -rwxr-xr-x root/root 382 2020-06-27 20:45 ./usr/bin/artic_mask -rwxr-xr-x root/root 412 2020-06-27 20:45 ./usr/bin/artic_plot_amplicon_depth -rwxr-xr-x root/root 394 2020-06-27 20:45 ./usr/bin/artic_vcf_filter -rwxr-xr-x root/root 392 2020-06-27 20:45 ./usr/bin/artic_vcf_merge -rwxr-xr-x root/root 384 2020-06-27 20:45 ./usr/bin/margin_cons -rwxr-xr-x root/root 398 2020-06-27 20:45 ./usr/bin/margin_cons_medaka -rwxr-xr-x root/root 382 2020-06-27 20:45 ./usr/bin/vcfextract drwxr-xr-x root/root 0 2020-06-27 20:45 ./usr/lib/ drwxr-xr-x root/root 0 2020-06-27 20:45 ./usr/lib/python3/ drwxr-xr-x root/root 0 2020-06-27 20:45 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2020-06-27 20:45 ./usr/lib/python3/dist-packages/artic/ -rw-r--r-- root/root 0 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/__init__.py -rw-r--r-- root/root 11516 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/align_trim.py -rw-r--r-- root/root 1461 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/align_trim_n.py -rw-r--r-- root/root 6585 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/align_trim_unit_test.py -rw-r--r-- root/root 1695 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/basecaller.py -rw-r--r-- root/root 1007 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/conftest.py -rw-r--r-- root/root 1404 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/demultiplex.py -rw-r--r-- root/root 1473 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/export.py -rw-r--r-- root/root 1724 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/extract.py -rw-r--r-- root/root 670 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/fasta_header.py -rw-r--r-- root/root 620 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/filter_reads.py -rw-r--r-- root/root 5576 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/gather.py -rw-r--r-- root/root 2717 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/guppyplex.py -rw-r--r-- root/root 7446 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/make_depth_mask.py -rw-r--r-- root/root 4202 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/margin_cons.py -rw-r--r-- root/root 5241 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/margin_cons_medaka.py -rw-r--r-- root/root 1619 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/mask.py -rw-r--r-- root/root 8210 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/minion.py -rw-r--r-- root/root 12849 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/minion_validator.py -rw-r--r-- root/root 10345 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/pipeline.py -rw-r--r-- root/root 855 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/pipeline_unit_test.py -rw-r--r-- root/root 5055 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/plot_amplicon_depth.py -rw-r--r-- root/root 1956 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/rampart.py -rw-r--r-- root/root 298 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/runs.py -rw-r--r-- root/root 3695 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/vcf_filter.py -rw-r--r-- root/root 1687 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/vcf_merge.py -rw-r--r-- root/root 2513 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/vcfextract.py -rw-r--r-- root/root 4963 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/vcftagprimersites.py -rw-r--r-- root/root 1835 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/vcftagprimersites_unit_test.py -rw-r--r-- root/root 22 2020-06-09 11:27 ./usr/lib/python3/dist-packages/artic/version.py drwxr-xr-x root/root 0 2020-06-27 20:45 ./usr/lib/python3/dist-packages/artic-1.1.3.egg-info/ -rw-r--r-- root/root 617 2020-06-27 20:45 ./usr/lib/python3/dist-packages/artic-1.1.3.egg-info/PKG-INFO -rw-r--r-- root/root 1 2020-06-27 20:45 ./usr/lib/python3/dist-packages/artic-1.1.3.egg-info/dependency_links.txt -rw-r--r-- root/root 508 2020-06-27 20:45 ./usr/lib/python3/dist-packages/artic-1.1.3.egg-info/entry_points.txt -rw-r--r-- root/root 1 2020-06-27 20:45 ./usr/lib/python3/dist-packages/artic-1.1.3.egg-info/not-zip-safe -rw-r--r-- root/root 0 2020-06-27 20:45 ./usr/lib/python3/dist-packages/artic-1.1.3.egg-info/requires.txt -rw-r--r-- root/root 6 2020-06-27 20:45 ./usr/lib/python3/dist-packages/artic-1.1.3.egg-info/top_level.txt drwxr-xr-x root/root 0 2020-06-27 20:45 ./usr/share/ drwxr-xr-x root/root 0 2020-06-27 20:45 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-06-27 20:45 ./usr/share/doc/python3-fieldbioinformatics/ -rw-r--r-- root/root 188 2020-06-27 20:45 ./usr/share/doc/python3-fieldbioinformatics/changelog.Debian.gz -rw-r--r-- root/root 1303 2020-06-09 11:27 ./usr/share/doc/python3-fieldbioinformatics/changelog.gz -rw-r--r-- root/root 1924 2020-06-27 20:45 ./usr/share/doc/python3-fieldbioinformatics/copyright moeller@steffen-laptop-debian:~/git/med-team/fieldbioinformatics/fieldbioinformatics-1.1.3$ On 27.06.20 20:43, Steffen Möller wrote:
Hello, I was after an idea about how the workflow packages for nextflow could possibly look like. There is no setup script, more like .install everything to the right location. The scripts with the .nf suffix indeed have a #!nextflow shebang line - let alone for help2man we need some preliminary nextflow package, I think. I admit to have somewhat given up on the capsule package. Maybe we can patch this out from the test routines somehow?!? I'll have a look. The original artic implementation is not by the nf-core folks but hidden in the "fieldbioinformatics" package of the artic-network. I added that package - maybe that is easier than finishing the artic nextflow package. And if we mean testing seriously, then should eventually compare the two implementations, right? I'll give that a shot, I think. Best, Steffen
