Dietmar Rieder

Paramter not correctly set when passing via config file

1

Hi, I noticed that the `-g` parameter of the `ext.args` in the `SUBREAD_FEATURECOUNTS` process is not set correctly when passing the `gencode` parameter via a config file e.g. `-c my_rnaseq.config`....

pureclip coredumps

6

Hi, the following pureclip command crashes with a coredump: pureclip -i umidedup.bam -bai umidedup.bam.bai -g homo_sapiens.88.fa -iv '1;2;3;4;8;16' -nt 8 -o PureCLIP.crosslink_sites.cov_CLmotifs.bed -nim 4 -fis fimo_clmotif_occurenc es.bed Last few output...

hide-modulefile is currently ignored

2

https://github.com/TACC/Lmod/blob/eb3e9119ef1ec3a17f2feb693c9dba16e1c93503/src/RC2lua.tcl#L65 The `hide-modulefile` function is currently ignored in TCL modules having `.modulerc` files since the function is a noop. In my simple minded approach I added basic functionality to it:...

Adding a timeout of 5 seconds to `smtplib.SMTP()` allows the script to continue when the port is blocking.

Solve issue with losing track of SLURM jobs using cephfs

5

The changes solve an issue with losing track of SLURM jobs on systems using cephfs when the number of jobs is high. Test case: running a pipeline that creates thousands...

Option to use TCRblosum for distance calculation

4

TCRblosum, a substitution matrix specifically derived from TCR sequences, is likely to provide a more accurate measure of TCR sequence similarity, however it is not yet used in scirpy. I...

Outdated HLA Class II models

2

> Thank you for your reply. I’ve been running the pipeline using a sample with both Class I and Class II HLA alleles supplied in the same format as your...