CasavaOneEightLanelessPerSampleDirFmt creates an invalid MANIFEST on import

[thermokarst]

Bug Description
The MANIFEST filepaths are missing the lane that is present in the actual imported files.

Screenshots

$ ls laneless
a_1_R1_001.fastq.gz b_2_R1_001.fastq.gz c_3_R1_001.fastq.gz

$ qiime tools import \
  --type 'SampleData[SequencesWithQuality]' \
  --input-path laneless \
  --source-format CasavaOneEightLanelessPerSampleDirFmt \
  --output-path demux.qza

$ qiime demux summarize \
  --i-data demux.qza \
  --o-visualization nope.qzv \
  --verbose
Plugin error from demux:

  [Errno 2] No such file or directory: '/var/folders/kv/fmn2vtxn5pq0c3tl9wv7cbqh0000gn/T/qiime2-archive-driuneqv/b9f3fa8d-7c4f-4ef6-8bb7-d2f5374d29e4/data/a_1_R1_001.fastq.gz'

$ qiime tools export demux.qza --output-dir lets-see && ls lets-see
MANIFEST                 a_1_L001_R1_001.fastq.gz b_2_L001_R1_001.fastq.gz c_3_L001_R1_001.fastq.gz metadata.yml

$ cat lets-see/MANIFEST
sample-id,filename,direction
a,a_1_R1_001.fastq.gz,forward
b,b_2_R1_001.fastq.gz,forward
c,c_3_R1_001.fastq.gz,forward

[ebolyen]

Whoops! Did someone finally need this variant again? Where/how did it come up?

[thermokarst]

Oops! Forgot to put the backref in the original issue:

Came up on the forum here.

[james-d]

Is this fixed (or going to be)? Or is there a permanent recommendation to use the manifest format?

[thermokarst]

Hi @james-d --- this hasn't been fixed yet, but it is still on our radar. PRs welcome 😉!