pblumenkamp / curare Goto Github PK

Rename repository to Curare

In GitLab by @[email protected] on Apr 23, 2018, 17:11

The database path must be relative. Absolute paths don't work at the moment.

In GitLab by @[email protected] on Apr 11, 2018, 16:54

DESeq2 should also save a normalized count table

In GitLab by @[email protected] on Mar 30, 2020, 11:32

Automatic preprocessing

https://github.com/OpenGene/fastp

The original issue

Id: 22
Title: Werden die ungemappten reads weggeschmissen?

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

The original issue

Id: 26
Title: [DESeq2] Empty first page in correlation heat map

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

In GitLab by @[email protected] on Jun 5, 2018, 09:54

Each run should save the version of each tool

The original issue

Id: 23
Title: readxplorer will relativen pfad haben. hier möglicher workaround

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

In GitLab by @[email protected] on Apr 23, 2018, 12:23

Optional settings in module config files should have a default value.

The original issue

Id: 30
Title: Sample name must not end with '_unmapped.bam'

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

The original issue

Id: 19
Title: unzip module

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

In GitLab by @[email protected] on Apr 11, 2018, 16:49

Switch from command line parameters to yaml config file

The original issue

Id: 11
Title: Bug or Feature: Screaming Files

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

In GitLab by @[email protected] on Jul 4, 2018, 13:35

Only related rules should restart after modifying the pipeline config.

In GitLab by @[email protected] on Jan 17, 2019, 12:54

Add STAR as an additional mapping tool

In GitLab by @[email protected] on Apr 11, 2018, 16:52

Create a setup for conda and make it downloadable from a conda channel

The original issue

Id: 35
Title: tests/resources/run.sh falscher Zugriff auf Array

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

The original issue

Id: 1
Title: add ReadXplorer rule

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

In GitLab by @[email protected] on Apr 23, 2018, 11:48

A module should have the possibility to have library files or scripts which have to be copied to the results folder too.

In GitLab by @rmueller on Jun 14, 2018, 11:32

for i in `ls ../../*/*/analysis/*/mapping/logs/bowtie2_mapping.*.log`; do
  echo -n $i" " >> tmp/mappings.log
  tail -n+2 $i | sed -e 's/^[^0-9]*\([0-9]\{1,\}\) (\([0-9.]\{1,\}\)%).*/\1\t\2/' | sed -e 's/^\(.*\)%.*$/\1/' | tr '\n' '\t' | sed -e 's/\t$//' >> tmp/mappings.log
  echo >> tmp/mappings.log
done

In GitLab by @[email protected] on Jun 8, 2018, 11:40

Files in config and groups file should be checked

In GitLab by @[email protected] on Apr 23, 2018, 17:48

Intermediate file of ReadXplorer import won't be deleted at the moment.

In GitLab by @[email protected] on Apr 11, 2018, 16:53

R scripts should save an r-dump after running

In GitLab by @rmueller on Jun 7, 2018, 15:10

In GitLab by @[email protected] on Apr 23, 2018, 11:48

Integrate DESeq2 as an analysis module

In GitLab by @[email protected] on Apr 23, 2018, 17:09

Add optional settings for bowtie2 module like local or global alignment or sensitivity.

In GitLab by @[email protected] on Apr 11, 2018, 16:58

Integrate a CI-runner for automatized testing

Adding support for 3rd generation sequencing files and adding mapping tools for long reads

In GitLab by @[email protected] on Mar 30, 2020, 11:30

Fast mapper

http://drive5.com/urmap/

The original issue

Id: 32
Title: YAML loader is deprecated

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

In GitLab by @cblume on Oct 15, 2019, 15:06

Merges conda_integration -> development

Conda-Integration vollständig. Tests laufen alle durch und brechen, wie zu erwarten, erst bei readexplorer ab.

In GitLab by @cblume on Oct 17, 2019, 12:21

Merges segemehl_module -> development

Segemehl-Modul läuft bei mir, wie gehabt, durch bis readexplorer.
Auch die Konvertierung zu TSV ist bereits vorhanden und ein Excel-Sheet wird ebenfalls erstellt. Allerdings sollte da nachgeschaut werden, ob das Ergebnis so ausreichend ist.

In GitLab by @[email protected] on Apr 11, 2018, 16:51

Create a requirements file.

Current known requirements:

• Minimal:

  • python3 (Version 3.5 or 3.6 must be tested)
  • Python packages
    • yaml
  • snakemake

• All (Minimal plus ...):

  • bowtie2
  • samtools
  • subread
  • readxplorer-cli
  • fastqc
  • multiqc
  • Python packages
    • pandas
    • xlsxwriter
  • R
    • DESeq2
    • ggplot2
    • reshape2
    • pheatmap

The original issue

Id: 34
Title: Typo: Ressources

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO

In GitLab by @[email protected] on Apr 11, 2018, 16:49

Add rule for FastQC/MultiQC

In GitLab by @cblume on Oct 24, 2019, 09:57

Merges conda_versions -> development

Wie besprochen:
Die Datei snakefiles/misc/parse_versions enthält eine Snakemake-Rule. Diese wird, zusammen mit den anderen Subworkflows, innerhalb von curare.py in die Datei Snakefile kopiert.
Diese Rule führt das Skript dge_pipeline/lib/parse_versions.py aus (welches im Laufe des Workflows nach output_dir/snakemake_lib/global_scripts kopiert wird). Dieses Skript ordnet, mittels Kommentaren mit den Modulnamen in den jeweiligen Environment-YAML-Dateien (<module>/lib/conda_env.yaml), die gehashten Environments den Modulen zu. Danach wird zu jedem Modul die Datei output_dir/.snakemake/conda/<environment_hash>/conda-meta/history geparsed und die primären und sekundären Abhängigkeiten, gruppiert nach Modul, in versions.yaml geschrieben. Diese Datei wird letztendlich unter output_dir/.report/ abgelegt.

In GitLab by @rmueller on Jan 21, 2020, 11:02

Die DESeq2 summary table muss überarbeitet werden. Zur Zeit filtert sie automatisch nach einem im Skript deklarierten Cutoff. Die einzelnen Schritte sollten auseinanderge"friemelt" werden. Des Weiteren soll nicht nur die gefilterte Summary table erstellt werden, sondern auch eine mit allen Features.

The original issue

Id: 25
Title: [DESeq2] Changing colors in featCount assignment plot

could not be created.
This is a dummy issue, replacing the original one. It contains everything but the original issue description. In case the gitlab repository is still existing, visit the following link to show the original issue:

TODO