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Requesting qcstats when none exist fails #113

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unode opened this issue Jul 4, 2019 · 0 comments
Closed

Requesting qcstats when none exist fails #113

unode opened this issue Jul 4, 2019 · 0 comments

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@unode
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unode commented Jul 4, 2019

Given:

ngless "1.0"
import "parallel" version "0.6"

samples = readlines("samplefile")
sample = lock1(samples)
input = samfile(sample + ".sam.gz")

collect(qcstats({fastq}), ofile="fqstats.txt", current=sample, allneeded=samples)
collect(qcstats({mapping}), ofile="mapstats.txt", current=sample, allneeded=samples)

This fails with:

[Thu 04-07-2019 13:47]: Script OK. Starting interpretation...
[Thu 04-07-2019 13:47] Line 5: lock1: Obtained lock file: 'ngless-locks/35ca1240/sample1.lock'
[Thu 04-07-2019 13:47] Line 5: Writing stats to 'ngless-stats/35ca1240/sample1'
Exiting after fatal error while loading and running script
Should Not Occur Error! This probably indicates a bug in ngless.
	Please get in touch with the authors with a description of how this happened.
	If possible run your script with the --trace flag and post the script and the resulting trace at 
		https://github.com/ngless-toolkit/ngless/issues
	or email us at [email protected].
Trying to merge a headerless file

It should just skip, create an empty file or fail with a better error message.

luispedro added a commit to luispedro/ngless that referenced this issue May 26, 2022
Several bugfixes included since beta1:

- Do not fail when merging empty files (ngless-toolkit#113)
- Fix version in install-reference mode (ngless-toolkit#107)
- Update --create-reference-pack mode (ngless-toolkit#108)
- Reset terminal colors after error for `--download-demo` mode
- Add --trace argument to all modes
luispedro added a commit to luispedro/ngless that referenced this issue May 30, 2022
Many bugfixes and improvements since `1.3.0`

- Do not fail when merging empty files (ngless-toolkit#113)
- Fix version in install-reference mode (ngless-toolkit#107)
- Update --create-reference-pack mode (ngless-toolkit#108)
- Reset terminal colors after error for `--download-demo` mode
- Add --trace argument to all modes
- Newer version of megahit
- Builtin gmgc module
- Faster internals
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