Updating setup-nextflow from 1 to 2

sanger-tol · Dec 5, 2024 · aa241a9 · aa241a9
1 parent e35a762
commit aa241a9
Show file tree

Hide file tree

Showing 8 changed files with 48 additions and 18 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -39,7 +39,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 

diff --git a/assets/github_testing/github_test.yaml b/assets/github_testing/github_test.yaml
@@ -16,7 +16,7 @@ ncbi_taxonomy_path: /home/runner/work/ascc/ascc/ncbi_taxdump/
 ncbi_ranked_lineage_path: /home/runner/work/ascc/ascc/ncbi_taxdump/rankedlineage.dmp
 busco_lineages_folder: /home/runner/work/ascc/ascc/busco_database
 busco_lineages: "diptera_odb10,insecta_odb10"
-fcs_gx_database_path: /home/runner/work/ascc/ascc/FCS_gx/
+fcs_gx_database_path: /home/runner/work/ascc/ascc/FCS_gx
 diamond_uniprot_database_path: /home/runner/work/ascc/ascc/diamond.dmnd
 diamond_nr_database_path: /home/runner/work/ascc/ascc/diamond.dmnd
 vecscreen_database_path: /home/runner/work/ascc/ascc/vecscreen/

diff --git a/assets/test.yaml b/assets/test.yaml
@@ -16,7 +16,7 @@ ncbi_taxonomy_path: /lustre/scratch123/tol/resources/taxonomy/latest/new_taxdump
 ncbi_ranked_lineage_path: /lustre/scratch123/tol/teams/tola/users/ea10/databases/taxdump/rankedlineage.dmp
 busco_lineages_folder: /lustre/scratch123/tol/resources/busco/latest/lineages/
 busco_lineages: "diptera_odb10,insecta_odb10"
-fcs_gx_database_path: /lustre/scratch124/tol/projects/asg/sub_projects/ncbi_decon/0.4.0/gxdb/
+fcs_gx_database_path: /lustre/scratch124/tol/projects/asg/sub_projects/ncbi_decon/0.4.0/gxdb
 vecscreen_database_path: /nfs/treeoflife-01/teams/tola/users/dp24/ascc/vecscreen/
 diamond_uniprot_database_path: /lustre/scratch123/tol/teams/tola/users/ea10/pipeline_testing/20240704_diamond_tiny_testdb/ascc_tinytest_diamond_db.dmnd
 diamond_nr_database_path: /lustre/scratch123/tol/teams/tola/users/ea10/pipeline_testing/20240704_diamond_tiny_testdb/ascc_tinytest_diamond_db.dmnd

diff --git a/conf/modules.config b/conf/modules.config
@@ -14,7 +14,6 @@ process {
 
     withName: SANGER_TOL_BTK {
         ext.args            = ""
-        ext.executor        = "bsub -Is -tty -e test.e -o test.log -n 2 -q oversubscribed -M1400 -R'select[mem>1400] rusage[mem=1400] span[hosts=1]'"
         ext.profiles        = "singularity,sanger"
         ext.get_versions    = "lsid | head -n1 | cut -d ',' -f 1"
         ext.version         = "0.6.0"

diff --git a/main.nf b/main.nf
@@ -16,6 +16,7 @@ nextflow.enable.dsl = 2
 */
 
 include { VALIDATE_TAXID            } from './modules/local/validate_taxid'
+include { COPY_FCS_GX               } from './modules/local/copy_fcs_tmp'
 
 include { ASCC_GENOMIC              } from './workflows/ascc_genomic'
 include { ASCC_ORGANELLAR           } from './workflows/ascc_organellar'
@@ -40,6 +41,7 @@ workflow SANGERTOL_ASCC_GENOMIC {
     validate_versions
     include_steps
     exclude_steps
+    fcs
 
     main:
 
@@ -51,7 +53,8 @@ workflow SANGERTOL_ASCC_GENOMIC {
         organelles,
         validate_versions,
         include_steps,
-        exclude_steps
+        exclude_steps,
+        fcs
     )
 }
 
@@ -65,6 +68,7 @@ workflow SANGERTOL_ASCC_ORGANELLAR {
     validate_versions
     include_steps
     exclude_steps
+    fcs
 
     main:
 
@@ -75,7 +79,8 @@ workflow SANGERTOL_ASCC_ORGANELLAR {
         samplesheet,
         validate_versions,
         include_steps,
-        exclude_steps
+        exclude_steps,
+        fcs
     )
 }
 /*
@@ -85,6 +90,9 @@ workflow SANGERTOL_ASCC_ORGANELLAR {
 */
 
 workflow {
+    //
+    // WORKFLOW: THIS WHOLE THING SHOULD BE IN A SUBWORKFLOW REALY
+    //
 
     main:
 
@@ -123,6 +131,25 @@ workflow {
     )
 
 
+    //
+    // TEMP MODULE: COPY FCS_GX_DB INTO TMP
+    //
+    include_workflow_steps  = params.include ? params.include.split(",") : "ALL"
+    VALID = ["ALL", "fcs-gx"]
+
+    if ( params.move_fcs && VALID.any{ include_workflow_steps.contains( it ) } ) {
+        COPY_FCS_GX (
+                params.fcs_gx_database_path,
+        )
+
+        fcs_gx_database_path = COPY_FCS_GX.out.fcsdb_path
+        delete_fcs = true
+    } else {
+        fcs_gx_database_path = Channel.of(params.fcs_gx_database_path)
+        delete_fcs = false
+    }
+
+
     //
     // WORKFLOW: Run main workflow for GENOMIC samples
     //
@@ -131,7 +158,8 @@ workflow {
         branched_assemblies.organellar_genome,
         VALIDATE_TAXID.out.versions,
         params.include,
-        params.exclude
+        params.exclude,
+        fcs_gx_database_path,
     )
 
 
@@ -165,6 +193,7 @@ workflow {
         VALIDATE_TAXID.out.versions,
         organellar_include,
         organellar_exclude,
+        fcs_gx_database_path
     )
 
     //

diff --git a/subworkflows/local/run_fcsgx.nf b/subworkflows/local/run_fcsgx.nf
@@ -17,10 +17,10 @@ workflow RUN_FCSGX {
             'all.gxi', 'all.gxs',  'all.taxa.tsv', 'all.meta.jsonl', 'all.blast_div.tsv.gz'
         )
         .combine(
-            Channel.of(fcsgxpath)
+            fcsgxpath
         )
         .map {suxfix, fcs_db ->
-            [file(fcs_db + '/' + suxfix)]
+            [file(fcs_db.toString() + '/' + suxfix)]
         }
         .collect()
         .set { fcsgxdb }

diff --git a/workflows/ascc_genomic.nf b/workflows/ascc_genomic.nf
@@ -43,11 +43,12 @@ include { methodsDescriptionText                        } from '../subworkflows/
 workflow ASCC_GENOMIC {
 
     take:
-    ch_samplesheet // channel: samplesheet read in from --input
-    organellar_genomes
+    ch_samplesheet          // channel: samplesheet read in from --input
+    organellar_genomes      // channel: tuple(meta, reference)
     validate_taxid_versions // Versions channel from main.nf
-    include_steps
-    exclude_steps
+    include_steps           // params.include_steps
+    exclude_steps           // params.exclude_steps
+    fcs_db                  // path(path)
 
     main:
     ch_versions = Channel.empty()
@@ -236,7 +237,7 @@ workflow ASCC_GENOMIC {
     if ( include_workflow_steps.contains('fcs-gx') || include_workflow_steps.contains('ALL') ) {
         RUN_FCSGX (
             ESSENTIAL_JOBS.out.reference_tuple_from_GG,
-            params.fcs_gx_database_path,
+            fcs_db,
             params.taxid,
             params.ncbi_ranked_lineage_path
         )

diff --git a/workflows/ascc_organellar.nf b/workflows/ascc_organellar.nf
@@ -42,10 +42,11 @@ include { methodsDescriptionText                        } from '../subworkflows/
 workflow ASCC_ORGANELLAR {
 
     take:
-    ch_samplesheet // channel: samplesheet read in from --input
+    ch_samplesheet          // channel: samplesheet read in from --input
     validate_taxid_versions // Versions channel from main.nf
-    include_steps
-    exclude_steps
+    include_steps           // params.include_steps
+    exclude_steps           // params.exclude_steps
+    fcs_db                  // path(file)
 
     main:
     ch_versions = Channel.empty()
@@ -189,7 +190,7 @@ workflow ASCC_ORGANELLAR {
     // if ( include_workflow_steps.contains('fcs-gx') || include_workflow_steps.contains('ALL') ) {
     //     RUN_FCSGX (
     //         ESSENTIAL_JOBS.out.reference_tuple_from_GG,
-    //         params.fcs_gx_database_path,
+    //         fcs_db,
     //         params.taxid,
     //         params.ncbi_ranked_lineage_path
     //     )