Skip to content

feat: nonpareil allow for empty FASTQ input files #4731

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
fgvieira wants to merge 11 commits into
base: master
Choose a base branch
from
Open

feat: nonpareil allow for empty FASTQ input files #4731

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
11 commits
Select commit Hold shift + click to select a range
58ca4a2
Add possible expected results
fgvieira Nov 20, 2025
671fcf6
Allow empty files as input
fgvieira Nov 20, 2025
14a6cc5
Fix tests and update env
fgvieira Nov 20, 2025
07cc8ca
Add missing tests
fgvieira Nov 20, 2025
e9ced1b
Fix NPO files
fgvieira Nov 21, 2025
3eaf43c
Code format
fgvieira Nov 21, 2025
8d5cdca
Add example to plot
fgvieira Nov 21, 2025
f4821e9
Fix NaN issue
fgvieira Nov 21, 2025
4dfd012
Remove JSON from expected results are they are not always identical
fgvieira Nov 21, 2025
26fab6b
Remove TSV from expected results are they are not always identical
fgvieira Nov 21, 2025
550b034
Merge branch 'master' into nonpareil_test
fgvieira Nov 21, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
89 changes: 44 additions & 45 deletions bio/nonpareil/infer/environment.linux-64.pin.txt
View file
Open in desktop

Large diffs are not rendered by default.

3 changes: 1 addition & 2 deletions bio/nonpareil/infer/environment.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,5 @@ channels:
- nodefaults
dependencies:
- nonpareil =3.5.5
- pigz
- pbzip2
- pbzip2 =1.1.13
- snakemake-wrapper-utils =0.8.0
21 changes: 21 additions & 0 deletions bio/nonpareil/infer/test/expected/a.fa.log
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
[ 0.0] Reducing query reads (-X) to 11
[ 0.0] WARNING: The kmer kernel implements an error correction function only compatible with FastQ
[ 0.0] Reading reads/a.fa
[ 0.0] Picking 11 random sequences
[ 0.0] Counting Kmers
[ 0.0] Read file with 15 sequences
[ 0.0] Average read length is 7.000000bp
[ 0.0] Sub-sampling library
[ 0.0] Sampling at 0.000000%
[ 0.0] Sampling at 11.764900%
[ 0.0] Sampling at 16.807000%
[ 0.0] Sampling at 24.010000%
[ 0.0] Sampling at 34.300000%
[ 0.0] Sampling at 49.000000%
[ 0.0] Sampling at 70.000000%
[ 0.0] Sampling at 100.000000%
[ 0.0] Evaluating consistency
[ 0.0] The coverage of this dataset is very high, and the precise value might be slighly off
[ 0.0] Not to be worried, this simply means that your dataset is too good to need heuristic estimates!
[ 0.0] WARNING: The curve reached near-saturation in 6 or fewer points, hence diversity estimations could be unreliable
[ 0.0] To increase the resolution of the curve increase -d, currently set at 0.700000
11 changes: 11 additions & 0 deletions bio/nonpareil/infer/test/expected/a.fa.npc
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
15
15
15
15
15
15
15
15
15
15
15
11 changes: 11 additions & 0 deletions bio/nonpareil/infer/test/expected/a.fas.bz2.npc
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
15
15
15
15
15
15
15
15
15
15
15
11 changes: 11 additions & 0 deletions bio/nonpareil/infer/test/expected/a.fasta.gz.npc
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
15
15
15
15
15
15
15
15
15
15
15
11 changes: 11 additions & 0 deletions bio/nonpareil/infer/test/expected/a.fastq.gz.npc
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
15
15
15
15
15
15
15
15
15
15
15
11 changes: 11 additions & 0 deletions bio/nonpareil/infer/test/expected/a.fq.bz2.npc
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
15
15
15
15
15
15
15
15
15
15
15
20 changes: 20 additions & 0 deletions bio/nonpareil/infer/test/expected/a.fq.log
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
[ 0.0] Reducing query reads (-X) to 11
[ 0.0] Reading reads/a.fq
[ 0.0] Picking 11 random sequences
[ 0.0] Counting kmers
[ 0.0] Read file with 15 sequences
[ 0.0] Average read length is 7.000000bp
[ 0.0] Sub-sampling library
[ 0.0] Sampling at 0.000000%
[ 0.0] Sampling at 11.764900%
[ 0.0] Sampling at 16.807000%
[ 0.0] Sampling at 24.010000%
[ 0.0] Sampling at 34.300000%
[ 0.0] Sampling at 49.000000%
[ 0.0] Sampling at 70.000000%
[ 0.0] Sampling at 100.000000%
[ 0.0] Evaluating consistency
[ 0.0] The coverage of this dataset is very high, and the precise value might be slighly off
[ 0.0] Not to be worried, this simply means that your dataset is too good to need heuristic estimates!
[ 0.0] WARNING: The curve reached near-saturation in 6 or fewer points, hence diversity estimations could be unreliable
[ 0.0] To increase the resolution of the curve increase -d, currently set at 0.700000
11 changes: 11 additions & 0 deletions bio/nonpareil/infer/test/expected/a.fq.npc
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
15
15
15
15
15
15
15
15
15
15
15
Loading
Loading