Db params

conf/test.config

@@ -30,11 +30,11 @@ params {
     taxon     = "Meles meles"
 
     // Databases
-    taxdump = "/lustre/scratch123/tol/resources/taxonomy/latest/new_taxdump"
-    busco   = "/lustre/scratch123/tol/resources/nextflow/busco/blobtoolkit.GCA_922984935.2.2023-08-03"
-    blastp  = "${projectDir}/assets/test/mMelMel3.1.buscogenes.dmnd"
-    blastx  = "${projectDir}/assets/test/mMelMel3.1.buscoregions.dmnd"
-    blastn  = "${projectDir}/assets/test/nt_mMelMel3.1"
+    taxdump = "https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz"
+    busco   = "https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/resources/blobtoolkit.GCA_922984935.2.2023-08-03.tar.gz"
+    blastp  = "https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/resources/mMelMel3.1.buscogenes.dmnd.tar.gz"
+    blastx  = "https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/resources/mMelMel3.1.buscoregions.dmnd.tar.gz"
+    blastn  = "https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/resources/nt_mMelMel3.1.tar.gz"
 
     // Need to be set to avoid overfilling /tmp
     use_work_dir_as_temp = true

conf/test_full.config

@@ -25,11 +25,11 @@ params {
     taxon     = "Laetiporus sulphureus"
 
     // Databases
-    taxdump = "/lustre/scratch123/tol/resources/taxonomy/latest/new_taxdump"
+    taxdump = "https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz"
     busco   = "/lustre/scratch123/tol/resources/busco/latest"
-    blastp  = "${projectDir}/assets/test_full/gfLaeSulp1.1.buscogenes.dmnd"
-    blastx  = "${projectDir}/assets/test_full/gfLaeSulp1.1.buscoregions.dmnd"
-    blastn  = "${projectDir}/assets/test_full/nt_gfLaeSulp1.1"
+    blastp  = "https://tolit.cog.sanger.ac.uk/test-data/Laetiporus_sulphureus/resources/gfLaeSulp1.1.buscogenes.dmnd"
+    blastx  = "https://tolit.cog.sanger.ac.uk/test-data/Laetiporus_sulphureus/resources/gfLaeSulp1.1.buscoregions.dmnd"
+    blastn  = "https://tolit.cog.sanger.ac.uk/test-data/Laetiporus_sulphureus/resources/nt_gfLaeSulp1.1"
 
     // Need to be set to avoid overfilling /tmp
     use_work_dir_as_temp = true

conf/test_raw.config

@@ -31,11 +31,11 @@ params {
     taxon     = "Meles meles"
 
     // Databases
-    taxdump = "/lustre/scratch123/tol/resources/taxonomy/latest/new_taxdump"
-    busco   = "/lustre/scratch123/tol/resources/nextflow/busco/blobtoolkit.GCA_922984935.2.2023-08-03"
-    blastp  = "${projectDir}/assets/test/mMelMel3.1.buscogenes.dmnd"
-    blastx  = "${projectDir}/assets/test/mMelMel3.1.buscoregions.dmnd"
-    blastn  = "${projectDir}/assets/test/nt_mMelMel3.1/"
+    taxdump = "https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz"
+    busco   = "https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/resources/blobtoolkit.GCA_922984935.2.2023-08-03.tar.gz"
+    blastp  = "https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/resources/mMelMel3.1.buscogenes.dmnd.tar.gz"
+    blastx  = "https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/resources/mMelMel3.1.buscoregions.dmnd.tar.gz"
+    blastn  = "https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/resources/nt_mMelMel3.1.tar.gz"
 
     // Need to be set to avoid overfilling /tmp
     use_work_dir_as_temp = true

modules.json

@@ -87,6 +87,11 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/seqtk/subseq/seqtk-subseq.diff"
                     },
+                    "untar": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "windowmasker/mkcounts": {
                         "branch": "master",
                         "git_sha": "32cac29d4a92220965dace68a1fb0bb2e3547cac",

modules/local/generate_config.nf

@@ -10,13 +10,11 @@ process GENERATE_CONFIG {
     val taxon_query
     val busco_lin
     path lineage_tax_ids
-    tuple val(meta2), path(blastn)
     val reads
-    // The following are passed as "val" because we just want to know the full paths. No staging necessary
-    val blastp_path
-    val blastx_path
-    val blastn_path
-    val taxdump_path
+    tuple val(meta2), path(blastp)
+    tuple val(meta3), path(blastx)
+    tuple val(meta4), path(blastn)
+    tuple val(meta5), path(taxdump)
 
     output:
     tuple val(meta), path("*.yaml")          , emit: yaml
@@ -43,10 +41,10 @@ process GENERATE_CONFIG {
         $accession_params \\
         --nt $blastn \\
         $input_reads \\
-        --blastp ${blastp_path} \\
-        --blastx ${blastx_path} \\
-        --blastn ${blastn_path} \\
-        --taxdump ${taxdump_path} \\
+        --blastp ${blastp} \\
+        --blastx ${blastx} \\
+        --blastn ${blastn} \\
+        --taxdump ${taxdump} \\
         --output_prefix ${prefix}
 
     cat <<-END_VERSIONS > versions.yml