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Update hands-on workshop to DSL2 #256

Merged
merged 29 commits into from
Aug 17, 2023
Merged

Update hands-on workshop to DSL2 #256

merged 29 commits into from
Aug 17, 2023

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mribeirodantas
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@mribeirodantas mribeirodantas commented Aug 16, 2023 •
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  • Update code editor and path to files
  • Add final script (converted to DSL2) + update Nextflow vesion in the outputs
  • Convert process 1A (prepare_genome_samtools) to DSL2 + content
  • Convert process 1B (prepare_genome_picard) to DSL2 + content
  • Convert process 1C (prepare_star_genome_index) to DSL2 + content
  • Convert process 1D (prepare_vcf_file) to DSL2 + content
  • Convert process 2 (rnaseq_mapping_star) to DSL2 + content
  • Convert process 3 (rnaseq_gatk_splitNcigar) to DSL2 + content
  • Convert process 4 (rnaseq_gatk_recalibrate) to DSL2 + content
  • Convert process 5 (rnaseq_call_variants) to DSL2 + content
  • Convert process 6 (ASE & RNA Editing) to DSL2 + content
    • post_process_vcf
    • prepare_vcf_for_ase
  • Convert chained channel operations to create grouped_vcf_bam_bai_ch to DSL2 + content
  • Convert process 7 (ASE_knownSNPs) to DSL2 + content
  • Test if the code works
  • Make sure instructions are correctly updated

@mribeirodantas
Update code editor and path to files
3a09085 
nano -> code
$HOME -> /workspace/gitpod/

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Add final script (converted to DSL2) + update Nextflow vesion in the
ee0c83f 
outputs

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Convert process 1A (prepare_genome_samtools) to DSL2
d33a881 
Also adapt the content to be up-to-date with the code converted
to DSL2.

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
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@mribeirodantas mribeirodantas mentioned this pull request Aug 16, 2023
Closed
@mribeirodantas
Prettify files
2ce610f 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas mribeirodantas self-assigned this Aug 16, 2023
@mribeirodantas mribeirodantas added documentation Improvements or additions to documentation enhancement New feature or request labels Aug 16, 2023
@mribeirodantas
Finish updating content around process 1A to DSL2
2cedc1e 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Convert process 1B (prepare_genome_picard) to DSL2
80c4639 
Also adapt the content to be up-to-date with the code converted
to DSL2.

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Fix highlighted lines in process 1B
f940f09 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Convert process 1C (prepare_star_genome_index) to DSL2
f751c87 
Also adapt the content to be up-to-date with the code converted
to DSL2.

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Fix note + highlights for process 1C
7de44c3 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Convert process 1D (prepare_vcf_file) to DSL2
db879e3 
Also adapt the content to be up-to-date with the code converted
to DSL2.

Also fix left BLANK issues in the previous processes

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Fix highlighting lines for process 1D
091e911 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Convert process 2 (rnaseq_mapping_star) to DSL2
2d13248 
Also adapt the content to be up-to-date with the code converted
to DSL2.

Remove quotes from process names up to process 2.

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Fix process 1D name
95ded31 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Convert process 3 (rnaseq_gatk_splitNcigar) to DSL2
0da6046 
Also adapt the content to be up-to-date with the code converted
to DSL2.

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Fix highlighting for solution of process 3
86d3a65 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Convert process 4 (rnaseq_gatk_recalibrate) to DSL2
6743bc1 
Also adapt the content to be up-to-date with the code converted
to DSL2.

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Convert process 5 (rnaseq_call_variants) to DSL2
b51330d 
Also adapt the content to be up-to-date with the code converted
to DSL2.

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Convert processes 6 (post_process_vcf and prepare_vcf_for_ase) to DSL2
ffd57c1 
Also adapt the content to be up-to-date with the code converted
to DSL2.

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas mribeirodantas force-pushed the update_dsl2_handson branch 3 times, most recently from 4e515d9 to 95f400d Compare August 17, 2023 01:46
@mribeirodantas
Prepare the grouped_vcf_bam_bai_ch channel for the next process
b720763 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Convert processes 7 (ASE_knownSNPs) to DSL2
a07e9a1 
Also adapt the content to be up-to-date with the code converted
to DSL2.

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas mribeirodantas linked an issue Aug 17, 2023 that may be closed by this pull request
Convert hands-on training to DSL2 #257
Closed
@mribeirodantas
Review 1st part (up to process 1D)
89afb14 
Remove remaining DSL1 code

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Fix minor/typos
5a35956 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Review process 2
ddd6279 
Process 2: Align RNA-Seq reads to the genome with STAR

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Update warning about previous workflow block
a41fa7c 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Review process 3
0b3df36 
Process 3: GATK Split on N

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Review process 4
87bf1c4 
Process 4: GATK Recalibrate

Replace $GATK occurrences by $params.gatk

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Review process 5
33438fd 
Process 5: GATK Variant Calling

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Review processes 6 and 7
67314c6 
Process 6: ASE & RNA Editing
Process 7: Allele-Specific Expression analysis with GATK ASEReadCounter

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Prettify
d53389d 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas mribeirodantas marked this pull request as ready for review August 17, 2023 04:09
christopher-hakkaart
christopher-hakkaart approved these changes Aug 17, 2023
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I haven't check it all works but it looks good.

Minor comment:

  • What do you think about using separate docker images for each tool/software?

@mribeirodantas
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What do you think about using separate docker images for each tool/software?
That's a great point, @christopher-hakkaart. I plan to do this in the next PR.

The goal of this PR is to make sure it works with DSL2 without changing much from the original logic. In the next PR, I plan to improve the content, and overall organization, add Gitpod instructions and improve things like this container suggestion. I totally agree we should have a samtools container image, a picard container image, a star container image, a vcftools container image, and then the GATK container image 😃

@mribeirodantas mribeirodantas merged commit 8fb73c1 into master Aug 17, 2023
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@mribeirodantas mribeirodantas deleted the update_dsl2_handson branch August 17, 2023 13:39
@mribeirodantas mribeirodantas removed the request for review from ewels August 17, 2023 13:51
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Convert hands-on training to DSL2
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@mribeirodantas @christopher-hakkaart