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Fix #638 [MAG_DEPTHS_PLOT fails if only a single bin is produced] #639

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merged 10 commits into from
Aug 16, 2024
Merged

Fix #638 [MAG_DEPTHS_PLOT fails if only a single bin is produced] #639

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3b95035
only make bin depths plots for cases w >2 samples and >2 bins
d-callan Jul 18, 2024
66a0af4
clarify when clustered heatmaps will be produced as outputs
d-callan Aug 9, 2024
f7c8aca
add bug fix 639 to changelog
d-callan Aug 9, 2024
bd3e813
[automated] Fix code linting
nf-core-bot Aug 10, 2024
6445d78
Merge branch 'dev' into fix-638
jfy133 Aug 15, 2024
83f1fe7
Add @d-callan and other recent code contributors
jfy133 Aug 15, 2024
f79135c
Add other third wave of developer leads to authors
jfy133 Aug 15, 2024
b708160
[automated] Fix code linting
nf-core-bot Aug 15, 2024
e7ebbfa
Update subworkflows/local/depths.nf
jfy133 Aug 15, 2024
36cfd42
Update LICENSE to include more recent contributors
jfy133 Aug 15, 2024
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11 changes: 10 additions & 1 deletion subworkflows/local/depths.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,14 @@ def getColNo(filename) {
return lines[0].split('\t').size()
}

/*
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* Get number of rows in a file
*/
def getRowNo(filename) {
lines = file(filename).readLines()
return lines.size()
}

workflow DEPTHS {
take:
bins_unbins //channel: val(meta), [ path(bins) ]
Expand Down Expand Up @@ -53,9 +61,10 @@ workflow DEPTHS {
.collectFile(name:'sample_groups.tsv'){ meta, reads -> meta.id + '\t' + meta.group + '\n' }

// Filter MAG depth files: use only those for plotting that contain depths for > 2 samples
// as well as > 2 bins
ch_mag_depths_plot = MAG_DEPTHS.out.depths
.map { meta, bin_depths_file ->
if (getColNo(bin_depths_file) > 2) [ meta, bin_depths_file ]
if (getColNo(bin_depths_file) > 2 && getRowNo(bin_depths_file) > 2) [ meta, bin_depths_file ]
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}

MAG_DEPTHS_PLOT ( ch_mag_depths_plot, ch_sample_groups.collect() )
Expand Down
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