Merge branch 'master' of ssh://git.scicore.unibas.ch:2222/zavolan_group/pipelines/rhea into polya_trimming_correction

MultiQC

See merge request zavolan_group/pipelines/rhea!49

Rhea naming

Closes #94

See merge request zavolan_group/pipelines/rhea!51

Substituted the samples.tsv new md5 in tests/test_scripts_labkey_to_snakemake_api/expected_output.md5

Modified test_scripts_labkey_to_snakemake_table to account for the modified samples.tsv
which now contains fq1_polya_3p, fq1_polya_5p, fq2_polya_3p, fq2_polya_5p instead of just
fq1_polya and fq2_polya.

In labkey_to_snakemake.py fixed the parameters so that there is 3p as well 5p polya
feature for every mate, which can be matched to the -a -g -A and -G options of cutadapt
depending on which is the sense or antisense mate the appropriate variable is populated
and the rest of variables are filled with 'XXXXXXXXXXXX' which leads to no trimming by
cutadapt. The poly-A trimming rules are fixed to contain all -a -g -A -G options.

Fix log file names

Closes #96

See merge request zavolan_group/pipelines/rhea!48

Update cluster.json

See merge request zavolan_group/pipelines/rnaseqpipeline!47

Changed adapter trimming parameters to fix overtrimming issues

Closes #92

See merge request zavolan_group/pipelines/rnaseqpipeline!46

fixed snakemake subworkflow typos/bugs

Closes #84

See merge request zavolan_group/pipelines/rnaseqpipeline!45

Documentation of pipeline steps

Closes #60 and #57

See merge request zavolan_group/pipelines/rnaseqpipeline!44

Dominik Burri authored 5 years ago and CJHerrmann committed 5 years ago

fixed typos

updated pipeline documentation

described seqmode specific rules

adapted to updates in Snakefile

moved star_rpm and samtools index to main snakefile description

linked README in documentation and vice versa

add TIN score merge and plot steps

See merge request zavolan_group/pipelines/rnaseqpipeline!43

Alfa integration

See merge request zavolan_group/pipelines/rnaseqpipeline!41

moved input_files into top-layer test directory for consistency.

corrected removal of test files

corrected md5sum for config.yaml

remove unnecessary file

- renaming bedgraph
- creating ALFA qc plots

removed conda dependence, moved import statement.

included ALFA in finish rule, corrected annotation.gtf and config.yaml, created new .svg

Simplify star_rpm & index_genomic_alignment_samtools.

See merge request zavolan_group/pipelines/rnaseqpipeline!38

Merged paired end and single end rules for star_rpm and index_genomic_alignment_samtools. Fixed wiring of calculate tin score: bam should be input and not params.

Replace cufflinks image with gffread image

Closes #85

See merge request zavolan_group/pipelines/rnaseqpipeline!37