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To use the motus module for newer versions, you need to download it and import it with 'local import'

1

Hi ``` conda create -n ngless source activate ngless ngless --download-demo gut-short (ngless) [ckzhu@vm-login02 gut-short]$ ngless gut-demo.ngl Exiting after fatal error while loading and running script Script Error (there is...

zckoo007

Hi Luis, I currently get an error I cannot trace back and our IT doesn't know what's the issue either. I am running a job on one of our huge...

uloeber

From the mailing list: ``` Hi all, since the latest NGLess release is v0.8.1 and the latest documented version v0.5.1 https://ngless.readthedocs.io/en/latest/releases.html https://ngless.readthedocs.io/en/latest/software.html as far as I can see, can anyone...

unode

Implement readset return type types for modules

2

We were trying to add a filtering step as an external module (having a read set as input and output). However, only counts and mapped read sets are supported at...

mkuhn

custom pattern recognition load_fastq_directory

1

extend the list of recognized patterns for paired reads (eg. R1/R2) or include optional space holder syntax for paired-end sequencing

uloeber

Error ir mapping step

7

Hi all. I am trying to test ngless with the examples for ocean's samples using this instruction: `ngless --threads=40 --index-path 'index' -t 'temp' ocean-demo.ngl . out` but I have the...

chodarq

`select()` currently supports an absolute threshold on match size, but user asks if it could support a relative one. Discussed on the mailing list: https://groups.google.com/g/ngless/c/Vq1fmnS5ZKU

luispedro

No HTML report is generated when using the parallel module

2

This can be seen when running for instance [the parallel test](https://github.com/ngless-toolkit/ngless/tree/master/tests/parallel) with `ngless --create-report -o report parallel.ngl`. The reason is that generating the final HTML report would require `collect()`ing reports...

unode

I have the following code human_mapped = map(input, reference='hg19') mapping_statistics = mapstats(human_mapped) collect(mapping_statistics, current=sample, allneeded=samples, ofile=QCDIR 'mapping_to_human.txt') In the output file I get the following sampe_1 sample_2 sample_3 sample_4 sample_5...

mettejoe

When using `parallel`, I've occasionally run into a situation where all locks are marked as `.finished` but `collect()` still reports `Cannot collect (not all files present yet)`. In this case...

unode