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Before read from file commit#13

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bwlang wants to merge 226 commits intomasternebiolabs/EM-seq:masterfrom before_read_from_file_commitnebiolabs/EM-seq:before_read_from_file_commitCopy head branch name to clipboard

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Commits on Apr 21, 2023

• scaffolded main modules and config

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• scaffold main modules and config

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Commits on Apr 23, 2023

• path_to_tiles,etc

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Commits on Apr 26, 2023

• cheap solution to filter on regex

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Commits on Apr 30, 2023

• test aggregation step

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• file shouldn't be here

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• WIP

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• Merge branch 'modular_dsl2' of github.com:nebiolabs/EM-seq into modular_dsl2

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Commits on May 1, 2023

• typos

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Commits on May 2, 2023

• quoted rg_id

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• samtools fastq needs -n when feeded to bwameth

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• nonconverted needed reference in args

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Commits on May 4, 2023

• working state keep comments

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• wip

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• except QC and outdated tools all good

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• ngs-agg stderr temporary saved

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Commits on May 5, 2023

• write ngs_agg out and err to files for record

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Commits on May 8, 2023

• pysam needs python10 in conda

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Commits on May 9, 2023

• library should be created in first step

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Commits on May 12, 2023

• alignment broken

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Commits on May 16, 2023

• WIP

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Commits on May 17, 2023

• getting aggregation ready (not yet)

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Commits on May 18, 2023

• passes tests

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• removed unnecessary comment

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• organize nextflow.config

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• publishdir should include flowcell in addition to library

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• Merge branch 'modular_dsl2' of github.com:nebiolabs/EM-seq into modular_dsl2

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• include module consistent with or without .nf

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• rails model expects no header for nonconverted_counts

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Commits on Jun 8, 2023

• before filtering by mapq before methylation analysis

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• mapq_filtered bams for methylation analysis

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Commits on Nov 29, 2023

• mapq20 on extract and analysis

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Commits on Nov 30, 2023

• workaround to vary wi.id

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Commits on Jan 10, 2024

• trimm reads to default=76

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Commits on Jan 18, 2024

• scripts in right place. Need delete old scripts

  aerijman

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Commits on Jan 21, 2024

• added metadata_fastq to ngs-agg

  aerijman

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• WIP

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• WIP

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• WIP

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• WIP

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• WIP

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• WIP

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• WIP

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• WIP

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Commits on Jan 23, 2024

• Workaround to remove ][ from barcode

  aerijman

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Commits on Feb 2, 2024

• conda specific chanels and versions

  aerijman

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Commits on Feb 7, 2024

• try mamba. conda is having trouble when run by determine_post_run

  aerijman

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Commits on Feb 8, 2024

• use mamba not conda

  aerijman

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Commits on Feb 11, 2024

• try usemamba set to true

  aerijman

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Commits on Feb 14, 2024

• mamba only picard was not created, hence added version and channel

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Commits on Feb 16, 2024

• add conda.cacheDir to nextflow config

  

  Seq Shepherd

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• get barcode from bam header

  

  Seq Shepherd

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Commits on Feb 21, 2024

• this is not available to everyone...

  

  Seq Shepherd

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Commits on Apr 1, 2024

• include fastp for aggregation

  aerijman

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Commits on Apr 11, 2024

• restructured to downsample with samtools

  aerijman

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  3b8e3cc

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• WIP

  aerijman

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  d968329

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• missing a comma...

  aerijman

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• path can not be empty. Trying null

  aerijman

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• path can not be null. Trying read2 same as read1 if not used

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  ac1e8da

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• path collition. Trying fake path

  aerijman

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  42167c4

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• path collition. Trying path to genome that is known and MUST exist

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• no need for variable

  aerijman

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• testing if def in assigning var value is a problem

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  0759e36

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• barcoode was groovy var but its bash

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• WIP

  aerijman

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  8729d73

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• wip

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  def917d

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• wip

  aerijman

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• samtools with no input when bam. fixed

  aerijman

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• added channel to tasmanian conda

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  ee6fa99

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• wip

  aerijman

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Commits on Apr 18, 2024

• DATABASE_ENV to RAILS_ENV

  aerijman

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• pattern to recognize read2 is more broad now.

  aerijman

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  d562a61

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• wip

  aerijman

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  53b24ca

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• wip

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  65ce013

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Commits on Apr 19, 2024

• recognitino of read2 from read1 improved

  aerijman

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Commits on Apr 23, 2024

• some barcodes are separated by + others -

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Commits on Apr 24, 2024

• wip

  aerijman

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  e88a7c5

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Commits on Apr 29, 2024

• add/replace RG if bam

  aerijman

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• RG as string not command

  aerijman

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Commits on May 1, 2024

• Will add a script to fix RG later

  aerijman

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• no header impacted samtools collate... how did it work before?

  aerijman

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Commits on May 14, 2024

• insert_size should include reads marked as duplicate

  aerijman

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Commits on Aug 27, 2024

• allow dag overwrite

  aerijman

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Commits on Aug 28, 2024

• signal 141 error hopeful fix

  

  Seq Shepherd

  committed
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Commits on Sep 4, 2024

• downsampling fastq fix

  aerijman

  committed
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Commits on Oct 18, 2024

• Merge branch 'master' into before_read_from_file_commit

  bwlang

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  329b2d7

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Commits on Oct 20, 2024

• package specification updates

  bwlang

  committed
  668f27a

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• adds support for next-seq 2000 poly-G trimming

  bwlang

  committed
  85c490d

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• avoid excess bam compression steps

  bwlang

  committed
  953e5c8

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Commits on Oct 21, 2024

• picard update to handle new argument syntax

  bwlang

  committed
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Commits on Oct 22, 2024

• no more fastq, only downsample if necessary

  bwlang

  committed
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Commits on Oct 28, 2024

• more cpus for alignment, allow sigpipe without failing the task

  bwlang

  committed
  04667f4

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• gc bias excluding controls

  aerijman

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  0c1ed63

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• wip

  

  Seq Shepherd

  committed
  9626168

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• dependency added

  

  Seq Shepherd

  committed
  305fa4c

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• fix syntax for samtools view with \-L option

  aerijman

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• harcoded genome by mistake

  aerijman

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Commits on Oct 29, 2024

• use bam header to select contigs to exclude in gcbias

  aerijman

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• syntax error

  aerijman

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  176a7e7

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• pipes samtools onto picard gc and exlcudes bed regions

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  a860e58

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• clean input parameters

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  51bdeb1

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• read length from data

  aerijman

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• no need to save to disk interleaved fq

  aerijman

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  a64a557

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• gzip out

  aerijman

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  11b51d0

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Commits on Oct 30, 2024

• pipe wait not loop and other PR things

  aerijman

  committed
  119743e

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• include the .bai file, write all bams to one directory, use /tmp for tmp (much faster)

  bwlang

  committed
  c2f38fe

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• simpler insert size combination, untested

  bwlang

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  503b5bd

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Commits on Oct 31, 2024

• avoid error 141

  aerijman

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  a7b5e85

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• simpler insert_size parser with mapq column

  aerijman

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  7c13c0d

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• interleaved fastq syntax was wrong

  aerijman

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  dc22fc9

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• fix outpu from alignment to markdups

  aerijman

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  7d46f58

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Commits on Nov 1, 2024

• removes unsued processes and out of date comments

  bwlang

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  1adc2b8

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• group by execution, not library

  bwlang

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  6c25de8

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• fast_qc -> fastqc

  bwlang

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  fca3916

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• comment fixes

  bwlang

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  e89b65b

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• whitespace, precise conda deps

  bwlang

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  e6bdb2b

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• adds multiqc

  bwlang

  committed
  aabf3a3

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• more cpus for alignment. dup marking

  bwlang

  committed
  98e95d9

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• whitespace

  bwlang

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  d9a5a56

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• get BC from RG header

  bwlang

  committed
  0032732

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Commits on Nov 2, 2024

• removes --barcode1, expects the bam to contain a BC tag instead

  bwlang

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  d636c9a

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• performance improvements and more modularization

  bwlang

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  0a9c064

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• corrects nextflow syntax warnings, comment/whitespace fixes

  bwlang

  committed
  f8d49ae

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• removes unused env

  bwlang

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  dfecab1

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• should not pipefail now

  bwlang

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  2199c11

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• missing import, correct process name

  bwlang

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  26cf90d

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• should not pipefail

  bwlang

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  47e45f1

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• debugging input channlel

  bwlang

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  32686a9

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• read2 has to be a valid path

  bwlang

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  60929d4

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• will a null work?

  bwlang

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  b53d22f

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• need a real path...

  bwlang

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  bf5b8ad

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• let's try a temp file...

  bwlang

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  705f762

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• needs to be a string...

  bwlang

  committed
  5d0dd9e

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• clearer syntax

  bwlang

  committed
  64eb0bf

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• stray )

  bwlang

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  ce3b724

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• buffer, not num tmp files

  bwlang

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  5adbcd3

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• correct instrument name and rg_line calculation

  bwlang

  committed
  460af64

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• switches to labels for config (friendlier for external users)

  Show description for a4f7e7b
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  a4f7e7b

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• typofix

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  a6118c1

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• pipefail should be on by default

  bwlang

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  67a7c88

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• fixing null memory object error?

  bwlang

  committed
  50be012

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• switching to correct nextflow.config

  bwlang

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  64cf57b

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• typofix

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  04f65c7

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Commits on Nov 3, 2024

• correct suffix for fastp log

  bwlang

  committed
  c3fe9bb

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• better resource partitioning between more and less cpu intensive components

  bwlang

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  e2634ee

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• updated picard syntax, more descriptive variable name

  bwlang

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  3a15ef3

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• // is not supported for integer division, mincpu for a task is 1

  bwlang

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  db805e1

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• removed inadvertant array constrution

  bwlang

  committed
  6b6fcdf

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• updates to consisten version of picard

  bwlang

  committed
  02afa3f

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Commits on Nov 4, 2024

• corrections and simplification of insert_size metrics calcs

  bwlang

  committed
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• need to wait for all the processes to finish to avoid a race

  bwlang

  committed
  58e6457

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• better separation of good insert_size files in the output

  bwlang

  committed
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Commits on Nov 5, 2024

• for join to work , all channels to have email and library first

  bwlang

  committed
  0e63097

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• remove unused params

  bwlang

  committed
  89f5c6b

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• need a stable file to avoid cache busting

  bwlang

  committed
  3082963

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• working aggregation code

  bwlang

  committed
  932441b

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• partially working multiqc

  bwlang

  committed
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Commits on Nov 8, 2024

• memory set for insert_Size_metrics

  

  Seq Shepherd

  committed
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• memory task simpler syntax in gcbias

  

  Seq Shepherd

  committed
  455c9e3

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• memory task simpler syntax in picard metrics

  

  Seq Shepherd

  committed
  a3bac0f

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• extra config is not needed

  

  Seq Shepherd

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  959d72b

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• missed flowcell...again...

  

  Seq Shepherd

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Commits on Nov 9, 2024

• signal 141 exit from head

  

  Seq Shepherd

  committed
  ed0b818

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• keep read_groups in bam header as a single line

  

  Seq Shepherd

  committed
  4136dfb

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Commits on Nov 11, 2024

• pipefail fixes mostly

  

  Seq Shepherd

  committed
  52ba00b

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• test files

  

  Seq Shepherd

  committed
  e6cfb77

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Commits on Nov 12, 2024

• extra empty line

  

  Seq Shepherd

  committed
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• remove metadata from aggregate results and rename output in insert size out channel

  

  Seq Shepherd

  committed
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• WIP: multiqc if not neb_internal and run_stript adapted to tests

  

  Seq Shepherd

  committed
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Commits on Nov 13, 2024

• run test script

  

  Seq Shepherd

  committed
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• tests seemingly passing

  

  Seq Shepherd

  committed
  852c9fa

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• internal_neb argument needed to be casted as a string

  

  Seq Shepherd

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  fee8002

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• missing a print in awk cant delived frac_reads

  

  Seq Shepherd

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  bd5e950

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• typos in downsampling

  

  Seq Shepherd

  committed
  f7b1e03

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Commits on Nov 14, 2024

• manage memory in processes

  

  Seq Shepherd

  committed
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Commits on Nov 15, 2024

• aggregation is default true

  

  Seq Shepherd

  committed
  04c24da

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• removal of suffix fastq or bam smarter

  

  Seq Shepherd

  committed
  f548bf5

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• removed comment

  

  Seq Shepherd

  committed
  7880d93

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Commits on Nov 16, 2024

• non-unique workflow in aggregation and unique ngs_agg.err-out

  

  Seq Shepherd

  committed
  0e4750a

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Commits on Nov 22, 2024

• downsample contained typos

  

  Seq Shepherd

  committed
  6fadb69

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Commits on Dec 2, 2024

• make sure we are guessing read2 from read1

  

  Seq Shepherd

  committed
  c67d831

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• gral fixes

  

  Seq Shepherd

  committed
  43a47d9

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Commits on Dec 3, 2024

• fix nextflow task variable call

  

  Seq Shepherd

  committed
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Commits on Dec 13, 2024

• path2ngs in config and allways multiqc

  aerijman

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• build ref index if needed and other stuff

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• add tests

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• option to generate index for genome

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• config works on sge and local too

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• option to generate index of genome part2

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• tests

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• github actions included

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Commits on Dec 23, 2024

• mac tr combined with /dev/urandom was not working

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Commits on Dec 24, 2024

• genome test is now correct

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Commits on Dec 25, 2024

• switches to nextflow action instead of conda + nextflow install

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• removes non-working secrets

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• adds missing samtools dependency

  bwlang

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• enables strict bash, trying to avoid false passing tests

  bwlang

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Commits on Dec 26, 2024

• explicit bash not sh for github actions

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Commits on Dec 27, 2024

• github actions not working with exported functions

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• conda to work in github and customer local

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• silly mistakes

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• WIP: test conda in github actions

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• WIP: dependencies

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• WIP: github actions dependencies

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• WIP: github actions dependencies...

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• revert test.yml and avoid mamba

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Commits on Jan 4, 2025

• WIP

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Commits on Jan 6, 2025

• mamba has problems in github actions

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• export fx inside run_test script

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• perhaps mkfifo negatively impacted exported fx

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• WIP

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Commits on Jan 8, 2025

• no /bin/bash if local. Only in github actions

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• clarify default input

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• added a little debugging

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