Add process to run get_unmerged

[dhoogest]

• generates expected outputs, but maybe is being called redundantly

I was testing this using params-ngs16s.json as follows:

dhoogest@gattaca:/molmicro/working/dhoogest/src/dada2-nf$ ./nextflow run main.nf -params-file params-ngs16s.json

Pipeline runs successfully and generates expected output:

dhoogest@gattaca:/molmicro/working/dhoogest/src/dada2-nf$ ls -lat output-single/dada/*/unmerged*
lrwxrwxrwx 1 dhoogest domain^users 106 Feb 23 10:49 output-single/dada/879-9/unmerged_R.fasta -> /mnt/disk15/molmicro/working/dhoogest/src/dada2-nf/work/37/1f9a4d1bbf0dfa5b25237958ec320a/unmerged_R.fasta
lrwxrwxrwx 1 dhoogest domain^users 106 Feb 23 10:49 output-single/dada/879-9/unmerged_F.fasta -> /mnt/disk15/molmicro/working/dhoogest/src/dada2-nf/work/37/1f9a4d1bbf0dfa5b25237958ec320a/unmerged_F.fasta
lrwxrwxrwx 1 dhoogest domain^users 106 Feb 23 10:49 output-single/dada/795-6/unmerged_F.fasta -> /mnt/disk15/molmicro/working/dhoogest/src/dada2-nf/work/3b/d382b57cae8d4304e28f52590821ab/unmerged_F.fasta
lrwxrwxrwx 1 dhoogest domain^users 106 Feb 23 10:49 output-single/dada/795-6/unmerged_R.fasta -> /mnt/disk15/molmicro/working/dhoogest/src/dada2-nf/work/3b/d382b57cae8d4304e28f52590821ab/unmerged_R.fasta
lrwxrwxrwx 1 dhoogest domain^users 106 Feb 23 10:49 output-single/dada/795-5/unmerged_R.fasta -> /mnt/disk15/molmicro/working/dhoogest/src/dada2-nf/work/0c/7ad3227ce45f4cd997dd067af3d036/unmerged_R.fasta
lrwxrwxrwx 1 dhoogest domain^users 106 Feb 23 10:49 output-single/dada/795-5/unmerged_F.fasta -> /mnt/disk15/molmicro/working/dhoogest/src/dada2-nf/work/0c/7ad3227ce45f4cd997dd067af3d036/unmerged_F.fasta
lrwxrwxrwx 1 dhoogest domain^users 106 Feb 23 10:49 output-single/dada/795-3/unmerged_R.fasta -> /mnt/disk15/molmicro/working/dhoogest/src/dada2-nf/work/c1/37fb621e0d68645bf1981a29b9579b/unmerged_R.fasta
lrwxrwxrwx 1 dhoogest domain^users 106 Feb 23 10:49 output-single/dada/795-3/unmerged_F.fasta -> /mnt/disk15/molmicro/working/dhoogest/src/dada2-nf/work/c1/37fb621e0d68645bf1981a29b9579b/unmerged_F.fasta
lrwxrwxrwx 1 dhoogest domain^users 106 Feb 23 10:49 output-single/dada/1029-38/unmerged_F.fasta -> /mnt/disk15/molmicro/working/dhoogest/src/dada2-nf/work/a0/fc0fcb288f9fe2edbd216fc63b6700/unmerged_F.fasta
lrwxrwxrwx 1 dhoogest domain^users 106 Feb 23 10:49 output-single/dada/1029-38/unmerged_R.fasta -> /mnt/disk15/molmicro/working/dhoogest/src/dada2-nf/work/a0/fc0fcb288f9fe2edbd216fc63b6700/unmerged_R.fasta
lrwxrwxrwx 1 dhoogest domain^users 106 Feb 23 10:49 output-single/dada/795-4/unmerged_F.fasta -> /mnt/disk15/molmicro/working/dhoogest/src/dada2-nf/work/4a/4fbf013c09a4249ab0f6a8e0f52129/unmerged_F.fasta
lrwxrwxrwx 1 dhoogest domain^users 106 Feb 23 10:49 output-single/dada/795-4/unmerged_R.fasta -> /mnt/disk15/molmicro/working/dhoogest/src/dada2-nf/work/4a/4fbf013c09a4249ab0f6a8e0f52129/unmerged_R.fasta

However, the counter for the process in the nextflow 'steps' (not sure what these are called) indicates 36, where I think there should only be 12 (6 .rds inputs, F/R each). Likely something I don't understand fully about specifying nextflow inputs/outputs - @nhoffman @crosenth lemme know if you have suggestions:

dhoogest@gattaca:/molmicro/working/dhoogest/src/dada2-nf$ ./nextflow run main.nf -params-file params-ngs16s.json
N E X T F L O W  ~  version 20.10.0
Launching `main.nf` [soggy_noether] - revision: 714ef7e750
executor >  local (73)
[04/0a83ac] process > copy_filelist          [100%] 1 of 1 ✔
[79/8e6e5d] process > read_manifest (1)      [100%] 1 of 1 ✔
[42/953437] process > plot_quality (4)       [100%] 6 of 6 ✔
[51/76ba1a] process > barcodecop_single (5)  [100%] 6 of 6 ✔
[d4/45076f] process > bcop_counts_concat     [100%] 1 of 1 ✔
[b4/5103a1] process > filter_and_trim (1)    [100%] 6 of 6 ✔
[9e/8ffbc9] process > learn_errors (1)       [100%] 3 of 3 ✔
[a8/efe171] process > dada_dereplicate (5)   [100%] 6 of 6 ✔
[37/1f9a4d] process > dada_get_unmerged (36) [100%] 36 of 36 ✔
[c0/2365da] process > combined_overlaps      [100%] 1 of 1 ✔
[c8/297da3] process > dada_counts_concat     [100%] 1 of 1 ✔
[57/1adccd] process > write_seqs             [100%] 1 of 1 ✔
[bc/e743d3] process > cmsearch               [100%] 1 of 1 ✔
[27/a22588] process > filter_svs             [100%] 1 of 1 ✔
[99/8378aa] process > join_counts            [100%] 1 of 1 ✔
[51/e15258] process > save_params            [100%] 1 of 1 ✔
Completed at: 23-Feb-2022 10:49:31
Duration    : 1m 37s
CPU hours   : 0.2
Succeeded   : 73

[dhoogest]

However, the counter for the process in the nextflow 'steps' (not sure what these are called) indicates 36, where I think there should only be 12 (6 .rds inputs, F/R each). Likely something I don't understand fully about specifying nextflow inputs/outputs - @nhoffman @crosenth lemme know if you have suggestions:

figured this out, I needed to use file instead of each .. see 68a664b

[nhoffman]

Thanks, @dhoogest - merging with one slight modification (f49a73d)