Comments (4)
Hi,
this issue should be fixed in the development version.
You can give it a try with nextflow run ... -r dev
. If it doesn't work, please let me know!
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Hi @grst I have been able now to test the dev pipeline. Thanks for the update. Unfortunately I am still facing validation issues:
I am using a single end dataset, where there is a fastq_1
, but there is not a fastq_2
.
The input.csv file is similar to:
"sample","fastq_1","fastq_2","strandedness",...
"id1","/path/to/fastq/sample1.fastq.gz","","auto",...
Please note how the fastq_2
column contains empty values.
I'm getting an error validating the 'input' again:
ERROR ~ ERROR: Validation of 'input' file failed!
-- Check '.nextflow.log' file for details
The following errors have been detected:
* -- Entry 1: Missing required value: fastq_2
* -- Entry 2: Missing required value: fastq_2
Having an empty fastq_2
seems correct to me when I check the code at the master
branch. There, if the fastq_2
is empty then the single_end
variable is set to "1"
. You can see this below (specifically line 184, in the not fastq_2
):
scrnaseq/bin/check_samplesheet.py
Lines 181 to 187 in 90cb6a4
However on the dev
branch, the input schema used for the fastq_2
validation must exist and can't be empty:
scrnaseq/assets/schema_input.json
Lines 16 to 30 in 1043441
I'd like for the scrnaseq pipeline to accept an input file with a fastq_2
column filled with ""
(empty strings), since that's what is generated by the nf-core/fetchngs
pipeline when downloading datasets.
Thanks and sorry for the delay in the reply
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Just for further ideas, it may be good to checkout the rnaseq pipeline:
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The check is done on purpose. All protocols supported by this pipeline use paired end data, where R1 contains UMI/barcode and R2 the actual sequence.
What kind of single-cell data are you dealing with?
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Related Issues (20)
- Samplesheet Check Bug HOT 1
- Flexible input read format with STARsolo with --soloBarcodeReadLength HOT 1
- Make scrnaseq pipeline v2.5.1 compatible with nextflow v22.04.0 HOT 1
- Clean up mtx conversion code
- Update to the latest simpleaf HOT 3
- allow use of .gz when specifying fast and gtf HOT 5
- Use compressed (gzip) fasta and gtf HOT 3
- cellranger_count.py: remove any existing output directory HOT 3
- Update cellranger modules to latest nf-core/modules versions HOT 1
- cellranger mkref with multiple species
- allow for extra columns in the sample sheet HOT 1
- Sample merging does not work if files are named the same
- 'star' in genome configrations ignored HOT 2
- Cellranger mkref resource flags incorrect HOT 3
- Error with CONCAT_H5AD HOT 3
- Running 'cellranger-arc count' with existing genome index
- cellranger-multi implementation follow-up
- Trimming R1 fast files in all aligners HOT 4
- Time limit of AlevinQC HOT 3
- Specify cellranger version HOT 1
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