Code

Nf phage finder#9

Code

Merged

aw-watson merged 42 commits intonf_annotationLANL-Bioinformatics/EDGEv3:nf_annotationfrom nf_phageFinderLANL-Bioinformatics/EDGEv3:nf_phageFinderCopy head branch name to clipboardSep 23, 2024

+1,336,510-31

Commits

Commits on Jul 1, 2024

• Early version. Not yet functional

  aw-watson

  committed
  be57915

Commits on Jul 2, 2024

• IDBA runs from NF script

  aw-watson

  committed
  b476074

Commits on Jul 3, 2024

• 4 of 5 assemblers running

  aw-watson

  committed
  f91da30

Commits on Jul 5, 2024

• all assemblers running

  aw-watson

  committed
  ef415fe

Commits on Jul 8, 2024

• Assemblers running. Graphs produced.

  aw-watson

  committed
  b939da8

Commits on Jul 9, 2024

• workflow now creates contigs for assembly

  aw-watson

  committed
  3333575

Commits on Jul 12, 2024

• Docker image for environment

  aw-watson

  committed
  1a51cb3

Commits on Jul 15, 2024

• Reduced Docker image size: 2.87GB->1.3GB

  aw-watson

  committed
  53aa4b1

Commits on Jul 16, 2024

• initial NF version

  aw-watson

  committed
  1d8d2a6

• runFaQCs now uses multistage build

  aw-watson

  committed
  5bf8798

• added test files in central location

  aw-watson

  committed
  fa8188b

Commits on Jul 17, 2024

• minor revisions

  aw-watson

  committed
  7f29a88

• variable definition

  aw-watson

  committed
  2dc63d7

• third-party requirement rework

  aw-watson

  committed
  4fdb0b0

Commits on Jul 22, 2024

• charliecloud now used to run sra2fastq and runFaQCs

  aw-watson

  committed
  c675ddf

• readsToContig now uses Charliecloud

  aw-watson

  committed
  fd09340

Commits on Jul 25, 2024

• taxonomy classification running against databases

  

  Andre Watson

  committed
  938e03a

Commits on Jul 26, 2024

• Initial Dockerfile

  aw-watson

  committed
  af4bb0b

Commits on Jul 29, 2024

• v1.0 Docker image

  aw-watson

  committed
  8fd6f09

• shifted execution of Krona prep scripts to workflow

  aw-watson

  committed
  e12522e

Commits on Jul 30, 2024

• attempt to resolve singularity write permissions

  aw-watson

  committed
  0634ccc

Commits on Aug 7, 2024

• Better matches EDGE output

  aw-watson

  committed
  3645606

Commits on Aug 8, 2024

• Attempts to rescue incomplete assemblies, similar to EDGE

  aw-watson

  committed
  b2c3d5f

Commits on Aug 12, 2024

• properly creates container converted to Singularity

  aw-watson

  committed
  4ecb0ab

Commits on Aug 14, 2024

• Runs all taxonomies in container

  aw-watson

  committed
  463fcf3

• fixed scripts to prevent container issues

  aw-watson

  committed
  c2af310

• Merge branch 'nf_readsTaxonomy' of https://github.com/LANL-Bioinformatics/EDGE_workflows into nf_readsTaxonomy

  aw-watson

  committed
  cc3bf97

Commits on Aug 15, 2024

• better matchingfor EDGE output

  aw-watson

  committed
  8ae4358

Commits on Aug 22, 2024

• Fixed issue in perl scripts causing errors when generating reports

  aw-watson

  committed
  b7b7d25

Commits on Aug 26, 2024

• Per discussions with Mark, prefer Singularity execution over Charliecloud

  aw-watson

  committed
  d990ebb

• Creating PDFs from SVGs

  aw-watson

  committed
  9f5ade8

• producing PDFs from SVG trees

  aw-watson

  committed
  a47ae79

• adding the actual svg2pdf script to bin

  aw-watson

  committed
  0465aed

• Merge branch 'nf_readsTaxonomy' of https://github.com/LANL-Bioinformatics/EDGE_workflows into nf_readsTaxonomy

  aw-watson

  committed
  85fc74d

Commits on Sep 3, 2024

• fixed heatmap generation

  aw-watson

  committed
  c97cf06

• cleanup

  aw-watson

  committed
  7eb69e7

Commits on Sep 16, 2024

• Merge pull request #6 from LANL-Bioinformatics/dockerReduction

  Show description for 20f99cc
  mflynn-lanl

  authored
  20f99cc

• Merge pull request #7 from LANL-Bioinformatics/nf_runAssembly

  Show description for 8fa630c
  mflynn-lanl

  authored
  8fa630c

• Merge pull request #8 from LANL-Bioinformatics/nf_readsTaxonomy

  Show description for b111107
  mflynn-lanl

  authored
  b111107

Commits on Sep 17, 2024

• basic pipeline

  aw-watson

  committed
  f3dc5b5

Commits on Sep 18, 2024

• working containerization

  aw-watson

  committed
  3c99563

• Publishing with correct structure. Matches existing EDGE test results.

  aw-watson

  committed
  5442168