carpentries-incubator snakemake-novice-bioinformatics issues

carpentries-incubator / snakemake-novice-bioinformatics

Introduction to Snakemake for Bioinformatics

https://carpentries-incubator.github.io/snakemake-novice-bioinformatics

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Update Workflows to Version 0.16.8

#72 carpentries-bot opened 1 month ago
1
Several concerns on Ep 11 (new assembly workflow)

#71 tbooth opened 2 months ago
3
Describe global and per-rule requirements

#70 tbooth opened 2 months ago
1
Clearer solution for Ep08

#69 tbooth closed 1 month ago
2
Break down ep05 into smaller tasks

#68 tbooth opened 3 months ago
0
Reconsider use of Figshare for the sample data

#67 tbooth opened 3 months ago
2
Solution to Ep07 does not work

#66 tbooth opened 3 months ago
1
Mention Snakemake wrappers

#65 tbooth closed 1 month ago
2
Introduce lists of inputs/outputs before named inputs and outputs

#64 tbooth opened 3 months ago
1
Use the log directive from the start

#63 tbooth opened 3 months ago
1
Be careful describing Kallisto and Salmon

#62 tbooth opened 3 months ago
4
Consider explicitly introducing "dot"

#61 tbooth opened 3 months ago
0
Chapter 4 solution does not work

#60 tbooth opened 4 months ago
1
Motivation for countreads rule

#59 tbooth opened 4 months ago
2
Consider not introducing -F as the default way to run Snakemake

#58 tbooth closed 4 months ago
2
Remove episode 13

#57 tbooth closed 4 months ago
1
Replace use of arithmetic in Bash

#56 tbooth closed 4 months ago
1
Bioinformatics concepts and best practise should be more thoroughly addressed

#55 tbooth opened 4 months ago
2
Update Workflows to Version 0.16.5

#54 carpentries-bot closed 1 month ago
1
Update Workflows to Version 0.16.3

#53 carpentries-bot closed 5 months ago
2
Clarifying how to use the editor

#52 tbooth opened 1 year ago
8
Improving the setup instructions - data

#51 tbooth closed 1 year ago
5
Introducing conda in the setup page

#50 tbooth opened 1 year ago
13
Relax the prerequisites for taking the lesson

#49 tbooth opened 1 year ago
1
Another option for formatting multi-line shell commands

#48 tbooth opened 1 year ago
2
Keeping up with Snakemake changes

#47 tbooth opened 1 year ago
2
Reconsider Putting output before input

#46 tbooth opened 1 year ago
1
Directories are automatically created for normal rules

#45 tbooth closed 1 year ago
1
Indentation is inconsistent

#44 tbooth closed 1 year ago
1
Sample wildcard is used for different things without a clear explanation

#43 tbooth closed 1 year ago
1
Improve the setup instructions

#42 tbooth closed 1 year ago
4
Better alt text for images

#41 tbooth closed 1 year ago
2
Note that the re-run triggers changed in Snakemake 7.8.0

#40 jdblischak closed 1 year ago
1
Fix typo in output directory name

#39 jdblischak closed 1 year ago
0
Addition to the Episode 9 for running Snakemake on the cluster

#38 tly0505 opened 1 year ago
1
urgent: fix workflows

#37 zkamvar closed 2 years ago
0
Change in Snakemake rerun behaviour

#36 ezherman closed 3 months ago
3
Fasta transcriptome file is described as a fastq

#35 mwhamgenomics closed 2 years ago
1
Edits to episodes 11 and 12

#34 ezherman closed 2 years ago
0
-n flag used without clarification

#33 ezherman closed 2 years ago
2
Remove mention of protected() because it's not very useful

#32 tbooth opened 2 years ago
1
Avoid use of shell wildcards when running Snakemake

#31 tbooth closed 2 years ago
0
Make it clear how to restore data files if they are clobbered

#30 tbooth closed 2 years ago
1
Avoid uncontrolled temporary files, and explain why

#29 tbooth closed 2 years ago
1
Lesson 2 exercise trick question

#28 tbooth closed 2 years ago
0
Clarify that Snakemake does not actually make any files - the DAG is just a plan

#27 tbooth closed 1 year ago
2
More visual depiction of Wildcards in ep2

#26 tbooth closed 2 years ago
2
Episodes are too long, especially ep. 6

#25 tbooth opened 2 years ago
3
Opening the MultiQC report on Macs

#24 lexnederbragt closed 2 years ago
0
symlinks issue multiqc

#23 lexnederbragt closed 2 years ago
2