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Updates, changes to flags and ci to allow for turning off btk
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@DLBPointon
DLBPointon committed Jul 12, 2024
1 parent 37c8847 commit 7e6eae7
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Showing 3 changed files with 20 additions and 39 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -139,4 +139,4 @@ jobs:
# For example: adding multiple test runs with different parameters
# Remember that you can parallelise this by using strategy.matrix
run: |
nextflow run ./sanger-ascc/${{ steps.branch-names.outputs.current_branch }}/main.nf -profile test,singularity --outdir ./results --steps ALL
nextflow run ./sanger-ascc/${{ steps.branch-names.outputs.current_branch }}/main.nf -profile test,singularity --outdir ./results --include ALL --exclude btk
4 changes: 2 additions & 2 deletions assets/test.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,8 +14,8 @@ dimensionality_reduction_methods: "pca,random_trees"
# "pca,umap,t-sne,isomap,lle_standard,lle_hessian,lle_modified,mds,se,random_trees,kernel_pca,pca_svd,autoencoder_sigmoid,autoencoder_linear,autoencoder_selu,autoencoder_relu,nmf"
nt_database: /lustre/scratch123/tol/teams/tola/users/ea10/pipeline_testing/20240704_blast_tiny_testdb/blastdb/
nt_database_prefix: tiny_plasmodium_blastdb.fa
nt_kraken_db_path: /lustre/scratch123/tol/teams/tola/users/ea10/ascc_databases/nt/nt
ncbi_accessionids_folder: /lustre/scratch123/tol/teams/tola/users/ea10/ascc_databases/ncbi_taxonomy/20230509_accession2taxid/
nt_kraken_db_path: /nfs/treeoflife-01/teams/tola/users/dp24/ascc/kraken2/kraken2/
ncbi_accessionids_folder: /nfs/treeoflife-01/teams/tola/users/dp24/ascc/20240709_tiny_accession2taxid/
ncbi_taxonomy_path: /lustre/scratch123/tol/resources/taxonomy/latest/new_taxdump
ncbi_rankedlineage_path: /lustre/scratch123/tol/teams/tola/users/ea10/databases/taxdump/rankedlineage.dmp
busco_lineages_folder: /lustre/scratch123/tol/resources/busco/data/v5/2021-08-27/lineages
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53 changes: 17 additions & 36 deletions workflows/ascc.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,8 @@ workflow ASCC {
ch_versions = Channel.empty()
ch_out_merge = Channel.empty()

workflow_steps = params.steps.split(",")
include_workflow_steps = params.include ? params.include.split(",") : ""
exclude_workflow_steps = params.exclude ? params.exclude.split(",") : ""

input_ch = Channel.fromPath(params.input, checkIfExists: true)

Expand Down Expand Up @@ -132,7 +133,7 @@ workflow ASCC {
// SUBWORKFLOW: COUNT KMERS, THEN REDUCE DIMENSIONS USING SELECTED METHODS
//

if ( workflow_steps.contains('kmers') || workflow_steps.contains('ALL')) {
if ( include_workflow_steps.contains('kmers') || include_workflow_steps.contains('ALL')) {

GENERATE_GENOME.out.reference_tuple
.map { meta, file ->
Expand Down Expand Up @@ -160,7 +161,7 @@ workflow ASCC {
//
// SUBWORKFLOW: EXTRACT RESULTS HITS FROM TIARA
//
if ( workflow_steps.contains('tiara') || workflow_steps.contains('ALL')) {
if ( include_workflow_steps.contains('tiara') || include_workflow_steps.contains('ALL')) {
EXTRACT_TIARA_HITS (
GENERATE_GENOME.out.reference_tuple
)
Expand All @@ -173,7 +174,7 @@ workflow ASCC {
//
// SUBWORKFLOW: EXTRACT RESULTS HITS FROM NT-BLAST
//
if ( workflow_steps.contains('nt_blast') || workflow_steps.contains('ALL') ) {
if ( include_workflow_steps.contains('nt_blast') || include_workflow_steps.contains('ALL') ) {
//
// NOTE: ch_nt_blast needs to be set in two places incase it
// fails during the run
Expand All @@ -193,7 +194,7 @@ workflow ASCC {
ch_nt_blast = []
}

if ( workflow_steps.contains('mito') || workflow_steps.contains('ALL') ) {
if ( include_workflow_steps.contains('mito') || include_workflow_steps.contains('ALL') ) {
//
// LOGIC: CHECK WHETHER THERE IS A MITO AND BRANCH
//
Expand All @@ -219,7 +220,7 @@ workflow ASCC {
ch_mito = []
}

if ( workflow_steps.contains('chloro') || workflow_steps.contains('ALL') ) {
if ( include_workflow_steps.contains('chloro') || include_workflow_steps.contains('ALL') ) {

//
// LOGIC: CHECK WHETHER THERE IS A PLASTID AND BRANCH
Expand Down Expand Up @@ -248,7 +249,7 @@ workflow ASCC {
//
// SUBWORKFLOW:
//
if ( workflow_steps.contains('fcs_adapt') || workflow_steps.contains('ALL') ) {
if ( include_workflow_steps.contains('fcs_adapt') || include_workflow_steps.contains('ALL') ) {
RUN_FCSADAPTOR (
YAML_INPUT.out.reference_tuple
)
Expand All @@ -266,7 +267,7 @@ workflow ASCC {
//
// SUBWORKFLOW:
//
if ( workflow_steps.contains('fcsgx') || workflow_steps.contains('ALL') ) {
if ( include_workflow_steps.contains('fcsgx') || include_workflow_steps.contains('ALL') ) {
RUN_FCSGX (
YAML_INPUT.out.reference_tuple,
YAML_INPUT.out.fcs_gx_database_path,
Expand All @@ -283,7 +284,7 @@ workflow ASCC {
//
// SUBWORKFLOW: IDENTITY PACBIO BARCODES IN INPUT DATA
//
if ( workflow_steps.contains('barcodes') || workflow_steps.contains('ALL') ) {
if ( include_workflow_steps.contains('barcodes') || include_workflow_steps.contains('ALL') ) {
PACBIO_BARCODE_CHECK (
YAML_INPUT.out.reference_tuple,
YAML_INPUT.out.pacbio_tuple,
Expand All @@ -308,7 +309,7 @@ workflow ASCC {
//
// SUBWORKFLOW: CALCULATE AVERAGE READ COVERAGE
//
if ( workflow_steps.contains('coverage') || workflow_steps.contains('busco_btk') || workflow_steps.contains('ALL') ) {
if ( include_workflow_steps.contains('coverage') || include_workflow_steps.contains('busco_btk') || include_workflow_steps.contains('ALL') ) {
RUN_READ_COVERAGE (
YAML_INPUT.out.reference_tuple,
YAML_INPUT.out.assembly_path,
Expand All @@ -326,7 +327,7 @@ workflow ASCC {
//
// SUBWORKFLOW: COLLECT SOFTWARE VERSIONS
//
if ( workflow_steps.contains('vecscreen') || workflow_steps.contains('ALL') ) {
if ( include_workflow_steps.contains('vecscreen') || include_workflow_steps.contains('ALL') ) {
RUN_VECSCREEN (
GENERATE_GENOME.out.reference_tuple,
YAML_INPUT.out.vecscreen_database_path
Expand All @@ -340,7 +341,7 @@ workflow ASCC {
//
// SUBWORKFLOW: Run the kraken classifier
//
if ( workflow_steps.contains('kraken') || workflow_steps.contains('ALL') ) {
if ( include_workflow_steps.contains('kraken') || include_workflow_steps.contains('ALL') ) {
RUN_NT_KRAKEN(
GENERATE_GENOME.out.reference_tuple,
YAML_INPUT.out.nt_kraken_db_path,
Expand All @@ -360,7 +361,7 @@ workflow ASCC {
//
// SUBWORKFLOW: DIAMOND BLAST FOR INPUT ASSEMBLY
//
if ( workflow_steps.contains('nt_diamond') || workflow_steps.contains('ALL') ) {
if ( include_workflow_steps.contains('nt_diamond') || include_workflow_steps.contains('ALL') ) {
NUCLEOT_DIAMOND (
modified_input,
YAML_INPUT.out.diamond_nr_database_path
Expand All @@ -377,7 +378,7 @@ workflow ASCC {
// SUBWORKFLOW: DIAMOND BLAST FOR INPUT ASSEMBLY
//
//qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids sscinames sskingdoms sphylums salltitles
if ( workflow_steps.contains('uniprot_diamond') || workflow_steps.contains('ALL') ) {
if ( include_workflow_steps.contains('uniprot_diamond') || include_workflow_steps.contains('ALL') ) {
UNIPROT_DIAMOND (
modified_input,
YAML_INPUT.out.diamond_uniprot_database_path
Expand Down Expand Up @@ -414,7 +415,7 @@ workflow ASCC {
//
// MODULE: AUTOFILTER ASSEMBLY BY TIARA AND FCSGX RESULTS
//
if ( workflow_steps.contains('tiara') && workflow_steps.contains('fcsgx') && workflow_steps.contains("autofilter") || workflow_steps.contains('ALL') ) {
if ( include_workflow_steps.contains('tiara') && include_workflow_steps.contains('fcsgx') && include_workflow_steps.contains("autofilter") || include_workflow_steps.contains('ALL') ) {
AUTOFILTER_AND_CHECK_ASSEMBLY (
YAML_INPUT.out.reference_tuple,
EXTRACT_TIARA_HITS.out.ch_tiara,
Expand Down Expand Up @@ -442,7 +443,7 @@ workflow ASCC {
// WE ARE USING THE PIPELINE HERE AS A MODULE THIS REQUIRES IT
// TO BE USED AS A AN INTERACTIVE JOB ON WHAT EVER EXECUTOR YOU ARE USING.
// This will also eventually check for the above run_btk boolean from autofilter
if ( workflow_steps.contains('busco_btk') && workflow_steps.contains("autofilter") && btk_bool.run_btk == "ABNORMAL" || workflow_steps.contains('ALL') ) {
if ( !exclude_workflow_steps.contains("btk") && include_workflow_steps.contains('busco_btk') && include_workflow_steps.contains("autofilter") && btk_bool.run_btk == "ABNORMAL" || !exclude_workflow_steps.contains("btk") && include_workflow_steps.contains('ALL') ) {

YAML_INPUT.out.reference_tuple
.combine(ch_bam)
Expand Down Expand Up @@ -483,26 +484,6 @@ workflow ASCC {
}


//
// SUBWORKFLOW: MERGES DATA THAT IS NOT USED IN THE CREATION OF THE BTK_DATASETS FOLDER
//
/* ASCC_MERGE_TABLES (
GC_CONTENT.out.txt, // FROM -- GC_COVERAGE.out.tsv
ch_coverage, // FROM -- RUN_COVERAGE.out.tsv.map{it[1]}
ch_tiara, // FROM -- TIARA_TIARA.out.classifications.map{it[1]}
[], // <-- BACTERIAL KRAKEN -- NOT IN PIPELINE YET
ch_kraken3, // FROM -- RUN_NT_KRAKEN.out.lineage.map{it[1]}
ch_nt_blast, // FROM -- EXTRACT_NT_BLAST.out.ch_blast_hits.map{it[1]}
ch_kmers, // FROM -- GET_KMERS_PROFILE.out.combined_csv
nt_hits, // FROM -- NUCLEOT_DIAMOND.out.reformed.map{it[1]}
un_hits, // FROM -- UNIPROT_DIAMOND.out.reformed.map{it[1]}
[], // <-- MARKER SCAN -- NOT IN PIPELINE YET
[], // <-- CONTIGVIZ -- NOT IN PIPELINE YET
CREATE_BTK_DATASET.out.create_summary.map{it[1]},
[], // <-- BUSCO_BTK -- NOT IN PIPELINE YET
ch_fcsgx // FROM -- PARSE_FCSGX_RESULT.out.fcsgxresult.map{it[1]}
) */

//
// SUBWORKFLOW: Collates version data from prior subworflows
//
Expand Down

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