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Converting Galaxy wf to Nextflow wf#1

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anilthanki wants to merge 159 commits intomainebi-gene-expression-group/scxa-tertiary-workflow:mainfrom feature/initial_wfebi-gene-expression-group/scxa-tertiary-workflow:feature/initial_wfCopy head branch name to clipboard

+1,160

Commits

Commits on Oct 25, 2024

• Update main.nf - adding wf process names

  anilthanki

  authored
  fdd8dc0

• Update main.nf - populate Column_rearrange processes

  anilthanki

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  fb359c8

• Update main.nf - populate mergeGeneFiles

  anilthanki

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  47d6662

• add nextflow.config for Slurm

  pmb59

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  f87d49b

• Update main.nf - moving input channels to workflow

  anilthanki

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  7169e98

• Update main.nf - deleting redundant input channels

  anilthanki

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  b7de140

• Update main.nf - adds wf step for mergeGeneFile

  anilthanki

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  aab1b63

• Update main.nf - adds workflow step for scanpy-read-10x

  anilthanki

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  681aeb5

• Update main.nf - fixing typo

  anilthanki

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  4cec90b

• Update main.nf - fixes input file names, process mergeGeneFiles and scanpy_read_10x

  anilthanki

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  9842c6a

Commits on Oct 28, 2024

• removes duplicated process and renames a file

  anilthanki

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  c23bb3a

• populate scanpy_filter_cells process

  anilthanki

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  2b039d0

• replaes anndata file name with var

  anilthanki

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  32731d0

• Populate scanpy_filter_genes process

  anilthanki

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  9de5090

• Adds missing quote

  anilthanki

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  772d841

• Populate normalise_data process

  anilthanki

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  f8ae27e

• Populate normalise_data_internal process

  anilthanki

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  c02a8c4

• Populate find_variable_genes process

  anilthanki

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  813c7ac

• Populate run_PCA process

  anilthanki

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  418610e

• Populate harmony_batch process

  anilthanki

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  e3e74b0

• Populate neighbours process

  anilthanki

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  9a23c62

• Applies batch_varibale

  anilthanki

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  e5e82e3

• Populate neighbours_for_umap process

  anilthanki

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  458a7b4

• removes random comment

  anilthanki

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  72c7473

• Fixes lint

  anilthanki

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  9632035

• Fixes input for neighbours_for_umap

  anilthanki

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  5272361

• Populate run_tsne process and fixes typo in neighbours_for_umap

  anilthanki

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  fae78f8

• Populate run_UMAP process

  anilthanki

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  e960f6e

Commits on Oct 30, 2024

• renames normalise_internal_data and adds container tag

  anilthanki

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  8342715

Commits on Oct 31, 2024

• Update main.nf - fixing join command for needed output

  anilthanki

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  3cc4066

• Update main.nf - sylink genes.tsv locally

  anilthanki

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  0d014f1

• Update main.nf - adding container tag and commenting param in filter_cell

  anilthanki

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  279b43c

• Update nextflow.config - adding singularity param

  anilthanki

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  f874a37

• Update main.nf - removing comment

  anilthanki

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  33f70da

• Update main.nf - adds container info fixes batch_variable

  anilthanki

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  1c924fb

• Update main.nf - fixes batch_variable condition, adds pca_param in neighbors_for_umap

  anilthanki

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  48f5f8d

Commits on Nov 1, 2024

• edit process run_umap

  pmb59

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  3f3fecb

• edit process run_tsne

  pmb59

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  a94177a

• edit process neighbours_for_umap

  Show description for 12efb95
  pmb59

  authored
  12efb95

Commits on Nov 4, 2024

• Update main.nf - fixes parallel run for neighbours_for_umap

  anilthanki

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  86de8ad

• Update main.nf - fixes process run_tsne

  anilthanki

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  8bf90e9

• fixes output run-tsne

  

  fg_atlas

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  b4d4ca2

• Update main.nf - populate find_clusters process

  anilthanki

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  fbf688e

• Update main.nf - fixes input for find_clusters

  anilthanki

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  ad54b02

• add nf-core linting github action

  pmb59

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  310c5b2

• fix lint command

  pmb59

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  8e459d1

• add java and nextflow to github action

  pmb59

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  cc5ea04

• Update main.nf - adds more params and logs

  anilthanki

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  1651976

• Update nextflow.config

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  anilthanki

  and

  pmb59

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  192ba0c

• Mov away from nf-core pipeline check, we only want to check the syntax in main.nf

  pmb59

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  2a26c09

• Update main.nf - ignores failed run and keeps only successful run

  anilthanki

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  5591c44

• fix nextflow syntax check

  pmb59

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  1900933

• Update main.nf

  anilthanki

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  f184945

• Update main.nf

  anilthanki

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  e0966f9

• Update main.nf - comments ignore error

  anilthanki

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  27359f6

• Update main.nf - fixed run_umap

  anilthanki

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  44b0e31

• Update main.nf - fixes run_umap

  anilthanki

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  79b2127

• Update main.nf - fixes run_umap

  anilthanki

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  a8319c1

• add simplified ci config

  pmb59

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  06c13b6

• disable CIi for now to avoid noise

  pmb59

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  8a50a17

• Update main.nf - adds parameter to neighbours_for_umap

  anilthanki

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  19c6658

• Update main.nf - fixes neighbours_for_umap

  anilthanki

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  216a89f

• Update main.nf - fixes neighbor spelling as per script name

  anilthanki

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  aa20bd6

• Update main.nf - fixes run_umap for neighbor key

  anilthanki

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  5b5a48b

Commits on Nov 5, 2024

• fixes umap

  

  fg_atlas

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  cf621e5

• populates find_markers process

  

  fg_atlas

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  806953a

• revert config changes

  

  fg_atlas

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  8f32220

• adds python script for final project process

  

  fg_atlas

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  bbfc882

• Update nextflow-linter.yaml - adding back changes pushed by @pmadrgal

  anilthanki

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  b9b1189

• Fixed filter_gene and filter_cell connections

  

  fg_atlas

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  d2b4a38

• changes permission

  

  fg_atlas

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  4b90e9f

• populate make_project_file process

  

  fg_atlas

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  4961d5f

• Update final_project.py - removing redundant code

  anilthanki

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  d02f1a3

• Update final_project.py - removes redundant code for uns_source files

  anilthanki

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  a010ff5

Commits on Nov 6, 2024

• Update final_project.py - removes redundant obs_source operations

  anilthanki

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  eb5a690

• Update main.nf - adds container in make_project_file process

  anilthanki

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  814df0b

• Update final_project.py

  anilthanki

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  376ad3a

• Update main.nf - fixinf make_project_file process

  anilthanki

  authored
  73eb167

• Update nextflow.config

  Show description for 9063a30
  

  anilthanki

  and

  pmb59

  authored
  9063a30

• Update main.nf

  Show description for 0dc94e5
  

  anilthanki

  and

  pmb59

  authored
  0dc94e5

• Update main.nf - now uses param dir_path param for input files

  anilthanki

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  b8cb996

• Create data_prep.sh

  anilthanki

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  9f512a9

• Update data_prep.sh - fixing log and force unzip

  anilthanki

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  2000f30

Commits on Nov 7, 2024

• Update main.nf - adds results dir

  anilthanki

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  ee8b177

• Update nextflow.config - temp commenting lines from config file

  anilthanki

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  47b6395

• Add draft processes and conditional for scrublet

  irisdianauy

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  82408ae

• Add param technology, change conditional

  irisdianauy

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  1b5847d

• Correct workflow

  irisdianauy

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  2b37608

• Rename scrublet process output

  irisdianauy

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  014601d

Commits on Nov 8, 2024

• Add real scrublet commands

  irisdianauy

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  02501d9

• Initialise batch variable, correct scrublet output format

  irisdianauy

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  8b74c49

Commits on Nov 12, 2024

• Allow scrublet to execute without a batch variable

  irisdianauy

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  ddb3916

• bash correction

  irisdianauy

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  3ec2fe6

• correct if expression

  irisdianauy

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  55feac5

Commits on Nov 13, 2024

• Filter predicted doublets if applicable

  irisdianauy

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  12f2024

• Update main.nf - adds restore_unscaled process - not tested

  anilthanki

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  130486f

• Create resource_unscalled.py

  anilthanki

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  2e19d39

• Update main.nf - adds missing (

  anilthanki

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  b5e37d1

• Update main.nf - adding processed_file back

  anilthanki

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  6bbf4cb

• Update main.nf - fixes restore_unscaled

  anilthanki

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  22d3728

• Update main.nf - addsmissin }

  anilthanki

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  77b50c2

• Rename resource_unscalled.py to restore_unscaled.py

  anilthanki

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  9fd8361

• Update main.nf - fixed mapping for find_marker after restore_unscaled

  anilthanki

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  75a57b0

• Update README.md

  anilthanki

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  2b539b7

• Update main.nf - adds publishDir options..

  anilthanki

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  db56ad6

• Update main.nf - fixes err

  anilthanki

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  96881dd

• Update main.nf - fixes err

  anilthanki

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  281875b

• Update main.nf - adds publishdir for scrublet plot

  anilthanki

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  6a2b736

Commits on Nov 15, 2024

• Update main.nf - redirects output to publishDir

  anilthanki

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  6b19a64

• Update main.nf

  anilthanki

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  040250c

• Update main.nf - removed filter_failed_umap/tsne as errorStrategy 'ignore' works

  anilthanki

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  82e3303

• Update main.nf - merge_embedings removed as TNSEs_ch.mix(UMAPs_ch).collect() does same thing

  anilthanki

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  73314b9

• Update main.nf - remove filtered_cellgroup_markers as errorStrategy 'ignore' does same thing

  anilthanki

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  7f9162f

• Update main.nf - merge_collection and build_list removed as its done by Nextfloe operator

  anilthanki

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  81b6e23

• Update main.nf - removed clustering_slot_names and merge_group_slotnames done by Nextflow operators

  anilthanki

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  7c4c139

• Update main.nf - removed meta_vars it was galaxy specific functionality

  anilthanki

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  c540cdf

• Update main.nf - removes hard coded name

  anilthanki

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  bce8436

• Update main.nf - adds missing )

  anilthanki

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  be5fcec

• Update main.nf - adds output_dir param

  anilthanki

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  bbcb763

• Update README.md

  anilthanki

  authored
  e81f6bc

Commits on Nov 19, 2024

• Update data_prep.sh - adds optional output dir

  anilthanki

  authored
  f32e525

• Update README.md - updates read me

  anilthanki

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  6c088d2

• Update main.nf - removes redundant comma

  anilthanki

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  ea27bba

• Update nextflow.config - adds config for reporting

  anilthanki

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  ffd6443

Commits on Nov 20, 2024

• Update nextflow.config - generates report in result_dir_path without specified in params

  anilthanki

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  23f0b6c

• Update main.nf - making batch_variable and pca_param as params.

  anilthanki

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  7ed1533

• Update main.nf - rename pca_param variable as representation

  anilthanki

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  52f75b3

• Update main.nf - renames output to match existing pipeline

  anilthanki

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  deb5506

• Update main.nf - parameterising container

  anilthanki

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  831982c

• Update main.nf - rename scanpy_container to scanpy_scripts_container

  anilthanki

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  9c05d8e

• Update README.md

  anilthanki

  authored
  05d3e75

• Update main.nf - rename output dir

  anilthanki

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  290d174

Commits on Nov 28, 2024

• Update main.nf

  anilthanki

  authored
  021411d

• Update main.nf

  anilthanki

  authored
  4a2af1f

Commits on Nov 29, 2024

• make scripts executable

  pmb59

  committed
  5d568d9

Commits on Dec 3, 2024

• Update main.nf - renaming tsne and umap tsvs

  anilthanki

  authored
  cc29b1f

• Update main.nf - updates output names

  anilthanki

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  9b89d11

• Update main.nf

  anilthanki

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  2d4e7e3

• Update main.nf - updates cluster file name to match existing and parsing script

  anilthanki

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  de3c4f4

• Update main.nf - fixes cluster output

  anilthanki

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  c300446

Commits on Dec 4, 2024

• Update main.nf - changes marker file name

  anilthanki

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  651119a

Commits on Dec 5, 2024

• Update main.nf - ads log

  anilthanki

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  a69967f

• Update main.nf - fixes marker rename

  anilthanki

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  af972a3

• Update main.nf - changes marker tsv name

  anilthanki

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  df76b9f

Commits on Dec 6, 2024

• Update main.nf - correct key added in run_umap

  irisdianauy

  authored
  98ae08e

• add _n in embeddings_neighbors_n_

  pmb59

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  6cb9451

Commits on Dec 10, 2024

• Update main.nf - adding log info

  anilthanki

  authored
  c24f6e1

• Update main.nf - filter cell process n_counts based on technology

  anilthanki

  authored
  0d3248c

Commits on Dec 11, 2024

• Add process scale_data

  irisdianauy

  committed
  7e61db3

Commits on Dec 12, 2024

• reorder params.neighbor_values

  pmb59

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  2806466

• Update main.nf

  pmb59

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  d420d39

• set env variable PYTHONIOENCODING = 'utf-8' for all processes

  pmb59

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  38766ea

• fix env PYTHONIOENCODING = 'utf-8'

  pmb59

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  18a690e

• Update main.nf

  pmb59

  authored
  8aece46

Commits on Dec 13, 2024

• ensure PYTHONIOENCODING='utf-8' on each scanpy-script command

  pmb59

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  9312311

Commits on Dec 18, 2024

• upgrade scanpy-scripts

  pmb59

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  27503b5

• pin production version of scanpy-scripts

  pmb59

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  ecdddb7

Commits on Dec 19, 2024

• upgrade s. scripts

  pmb59

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  c2a2852

Commits on Dec 20, 2024

• specify a Singularity cache directory

  pmb59

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  ef03cda