Closed mapo9 closed 2 months ago
Currently we have the problem that (for single cell data), the workflow fails at the SINGLE_CELL_QC_AND_FILTERING:SINGLE_CELL_QC
step with the following error
Quitting from lines 210-213 [removeDoublets] (_main.Rmd)
Error in removeDoublets():
! The column cell_id contains no data
Backtrace:
1. enchantr::removeDoublets(...)
Warning messages:
1: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'enchantr'
2: replacing previous import 'data.table::last' by 'dplyr::last' when loading 'enchantr'
3: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'enchantr'
Execution halted
Work dir:
/home/kymmp01/workdir/pipeline_dev/trust42airrflow/airrflow/test_flow/work/40/5d32e7d034d6123f08d2cc50bda49f
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
-- Check '.nextflow.log' file for details
ERROR ~ Corruption:
Descriptor does not contain a meta-nextfile entry
Descriptor does not contain a meta-lognumber entry
Descriptor does not contain a last-sequence-number entry
-- Check '.nextflow.log' file for details
I am pretty sure this happens because ! The column cell_id contains no data
.
Currently, I am using the OUT_airr.tsv
to feed the TRUST4 results into the immcantation workflow.
Here, each sequence
is one row.
TRUST4 also provides a out_barcode_airr.tsv
for single cell data where each cell_id
is one row.
So basically this gives clonotypes for a barcode with "consensus_count" being the number of reads/UMI supporting this contig. Obviously, the barcode_airr is a lot larger and contains many redundant junctions when different cells present the same clone.
I think we have 2 options now:
The discussion with the TRUST4 developers about this can be found here.
This might also help understand:
nf-core lint
overall result: Failed :x:Posted for pipeline commit 6f9e5af
+| ✅ 206 tests passed |+
#| ❔ 6 tests were ignored |#
!| ❗ 1 tests had warnings |!
-| ❌ 1 tests failed |-
I worked some more on this issue and tested the barcode_airr
file now as well. This contains cell_ids
and the Immcantation frameworks in airrflow runs through fine using this file.
I am adding the test airr files here as well.
Here you can also find the respective airrflow results.
It would be great, if you could have a look whether the results look reasonable for you like this or if we need to find another solution for the integration of TRUST4.
This PR adds the TRUST4 module in a new subworkflow.
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).