snakemake-rna-seq issueshttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues2020-09-10T15:32:12+02:00https://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/1paired-end mode "InputFiles" object has no attributes "fq1"2020-09-10T15:32:12+02:00Aurélien Ginolhacpaired-end mode "InputFiles" object has no attributes "fq1"https://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/2technical replicates from units are not collapsed2020-09-10T15:32:12+02:00Aurélien Ginolhactechnical replicates from units are not collapsedeither at
- the mapping step
- in featureCounts by summing counts
- in deseq init with CollapseReplicateseither at
- the mapping step
- in featureCounts by summing counts
- in deseq init with CollapseReplicateshttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/3featuresCount not prepare to deal with paired-end reads2020-09-17T16:22:53+02:00Aurélien GinolhacfeaturesCount not prepare to deal with paired-end readshttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/4check if samples are congruent between units.tsv and samples.tsv2020-10-02T11:57:33+02:00Aurélien Ginolhaccheck if samples are congruent between units.tsv and samples.tsvcheck if samples are identical between units.tsv and samples.tsvcheck if samples are identical between units.tsv and samples.tsvhttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/5makes dashes forbidden, or replace automatically by underscores2020-10-02T10:37:17+02:00Aurélien Ginolhacmakes dashes forbidden, or replace automatically by underscores```
[1] "orginal contrast condition_CTRL-90_vs_CTRL-smNPC"
[1] "available contrast Intercept"
[2] "available contrast condition_CTRL_30_vs_CTRL_120"
[3] "available contrast condition_CTRL_60_vs_CTRL_120"
``````
[1] "orginal contrast condition_CTRL-90_vs_CTRL-smNPC"
[1] "available contrast Intercept"
[2] "available contrast condition_CTRL_30_vs_CTRL_120"
[3] "available contrast condition_CTRL_60_vs_CTRL_120"
```https://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/6fastq_screen wrapper is not dealing with `seq` in fastq names2023-08-25T13:12:12+02:00Aurélien Ginolhacfastq_screen wrapper is not dealing with `seq` in fastq namesthis line from the wrapper:
```
>>> re.split(".fastq|.fq|.txt|.seq", os.path.basename("fastq/RNAseqForm_8h_3_Elisabeth_S8_R1_001.fastq.gz"))
['RN', 'Form_8h_3_Elisabeth_S8_R1_001', '.gz']
```
will poorly split the fastq name and prevent ...this line from the wrapper:
```
>>> re.split(".fastq|.fq|.txt|.seq", os.path.basename("fastq/RNAseqForm_8h_3_Elisabeth_S8_R1_001.fastq.gz"))
['RN', 'Form_8h_3_Elisabeth_S8_R1_001', '.gz']
```
will poorly split the fastq name and prevent the mv of correct resultshttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/7cannot trim with more than one adapter2021-06-11T14:36:31+02:00Aurélien Ginolhaccannot trim with more than one adapter`AdapterRemoval` can use a file for trim with > 1 adapter.
Filipe found a nice solution [in his wrapper](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/adapterremoval.html)
quick and dirty solution in `/work/projects/hncf...`AdapterRemoval` can use a file for trim with > 1 adapter.
Filipe found a nice solution [in his wrapper](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/adapterremoval.html)
quick and dirty solution in `/work/projects/hncfp` missing assertion files `adapters.txt` existAurélien GinolhacAurélien Ginolhachttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/8container should one specified once in Snakefile2021-11-26T15:05:22+01:00Aurélien Ginolhaccontainer should one specified once in Snakefileand not in all rulesand not in all rulesAurélien GinolhacAurélien Ginolhachttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/9featureCounts cannot deal with BAMs in both SE and PE2021-11-26T16:11:56+01:00Aurélien GinolhacfeatureCounts cannot deal with BAMs in both SE and PEhttps://support.bioconductor.org/p/98978/#98996
should be run twice and merge afterwardshttps://support.bioconductor.org/p/98978/#98996
should be run twice and merge afterwardsAurélien GinolhacAurélien Ginolhachttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/10new deseq2 check counts column names2021-12-01T16:51:17+01:00Aurélien Ginolhacnew deseq2 check counts column namesDESeq2 v1.34.0DESeq2 v1.34.0https://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/11check that samples in any config files are not duplicated2022-07-26T14:42:35+02:00Aurélien Ginolhaccheck that samples in any config files are not duplicated
For example detect those mistakes:
```
T4H-B6 1 fastq/T4H-B6_drna_FUSR3_MDM_S7_R1_001.fastq.gz NA reverse
T4HFN-B6 1 fastq/T4HFN-B6_drna_FUSR3_MDM_S8_R1_001.fastq.gz NA reverse
T24H-B6 1 fast...
For example detect those mistakes:
```
T4H-B6 1 fastq/T4H-B6_drna_FUSR3_MDM_S7_R1_001.fastq.gz NA reverse
T4HFN-B6 1 fastq/T4HFN-B6_drna_FUSR3_MDM_S8_R1_001.fastq.gz NA reverse
T24H-B6 1 fastq/T24H-B6_drna_FUSR3_MDM_S9_R1_001.fastq.gz NA reverse
T24HFN-B6 1 fastq/T24HFN-B6_drna_FUSR3_MDM_S10_R1_001.fastq.gz NA reverse
T24HFN-B6 1 fastq/T24HFN-B6_drna_FUSR3_MDM_S10_R1_001.fastq.gz NA reverse
```
`T24HFN-B6` is present twiceAurélien GinolhacAurélien Ginolhachttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/12more strict on the units.tsv / samples.tsv2022-07-25T15:52:45+02:00Aurélien Ginolhacmore strict on the units.tsv / samples.tsv
- test number of columns, any extra should be an error
- test if no file are duplicated **among** `R1` **AND** `R2`
- test number of columns, any extra should be an error
- test if no file are duplicated **among** `R1` **AND** `R2`Aurélien GinolhacAurélien Ginolhachttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/13logs of fastqc are not written2022-07-22T15:10:32+02:00Aurélien Ginolhaclogs of fastqc are not writtenAurélien GinolhacAurélien Ginolhachttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/14add tests via CI2023-09-06T10:27:18+02:00Aurélien Ginolhacadd tests via CImaybe like in https://git-r3lab.uni.lu/IMP/imp3/-/blob/master/.gitlab-ci.ymlmaybe like in https://git-r3lab.uni.lu/IMP/imp3/-/blob/master/.gitlab-ci.ymlhttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/15units.tsv, standeness shoud not be empty2022-08-26T15:23:48+02:00Aurélien Ginolhacunits.tsv, standeness shoud not be emptyfill out by at least nonefill out by at least nonehttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/16checkpoint tutorial for diverting branches2023-08-22T16:59:45+02:00Aurélien Ginolhaccheckpoint tutorial for diverting brancheshttps://github.com/weber8thomas/snakemake_tutorials/tree/main/checkpoint
https://twitter.com/weber8thomas/status/1562178119632568321?s=20&t=xFXdwKDpKZL0RZdUxdnCBg
![](https://pbs.twimg.com/media/Fa34sLjXkAEEgQe?format=jpg&name=medium)https://github.com/weber8thomas/snakemake_tutorials/tree/main/checkpoint
https://twitter.com/weber8thomas/status/1562178119632568321?s=20&t=xFXdwKDpKZL0RZdUxdnCBg
![](https://pbs.twimg.com/media/Fa34sLjXkAEEgQe?format=jpg&name=medium)https://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/17add screenplot to pca.pdf2023-08-22T16:52:50+02:00Aurélien Ginolhacadd screenplot to pca.pdfAurélien GinolhacAurélien Ginolhachttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/18reduce number of threads for align_multi2023-04-25T12:59:17+02:00Aurélien Ginolhacreduce number of threads for align_multionly 2 samples in parallel for iris nodesonly 2 samples in parallel for iris nodesAurélien GinolhacAurélien Ginolhachttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/19implement the nice updates in v2 of the original template2023-05-02T10:40:40+02:00Aurélien Ginolhacimplement the nice updates in v2 of the original templateespically the deseq2 upgrade
https://github.com/snakemake-workflows/rna-seq-star-deseq2/releases/tag/v2.0.0espically the deseq2 upgrade
https://github.com/snakemake-workflows/rna-seq-star-deseq2/releases/tag/v2.0.0Aurélien GinolhacAurélien Ginolhachttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/20missing readspergene out with new wrapper2023-11-02T09:26:54+01:00Aurélien Ginolhacmissing readspergene out with new wrapper```
rule align_multi:
input:
# this function is called as many samples are provided in output
# technical replicates are merged in STAR
fq1 = get_fq1,
fq2 = get_fq2, # optional, return none if not in u...```
rule align_multi:
input:
# this function is called as many samples are provided in output
# technical replicates are merged in STAR
fq1 = get_fq1,
fq2 = get_fq2, # optional, return none if not in units.tsv
idx = rules.star_index.output
output:
aln="star/{sample}/Aligned.sortedByCoord.out.bam",
log="logs/star/{sample}/Log.out",
log_final="logs/se/{sample}/Log.final.out",
sj="star/{sample}/SJ.out.tab",
reads_per_gene= "star/{sample}/ReadsPerGene.out.tab"
log:
"logs/star/{sample}.log"
```Aurélien GinolhacAurélien Ginolhac