Merge pull request #575 from nf-core/temp-test-full-profile

Temporary test full profile (until container and tax anno reference files fixed)

Author: jfy133

CHANGELOG.md

@@ -9,8 +9,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- [#575](https://github.com/nf-core/mag/pull/575/files) - Deactivated MetaSPAdes, Centrifuge, and GTDB in test_full profile due to some container incompatibilities in nf-core megatest AWS configurations (by @jfy133)
+
 ### `Fixed`
 
+- [#574](https://github.com/nf-core/mag/pull/574) - Fix wrong channel going to BIN_SUMMARY (fix by @maxibor)
+
 ### `Dependencies`
 
 ### `Deprecated`

conf/test_full.config

@@ -19,15 +19,21 @@ params {
     host_fasta    = "s3://ngi-igenomes/test-data/mag/hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz"
     input         = "s3://ngi-igenomes/test-data/mag/samplesheets/samplesheet.full.csv"
 
-    centrifuge_db = "s3://ngi-igenomes/test-data/mag/p_compressed+h+v.tar.gz"
+    //centrifuge_db = "s3://ngi-igenomes/test-data/mag/p_compressed+h+v.tar.gz"
     kraken2_db    = "s3://ngi-igenomes/test-data/mag/minikraken_8GB_202003.tgz"
     cat_db        = "s3://ngi-igenomes/test-data/mag/CAT_prepare_20210107.tar.gz"
-    gtdb_db       = "s3://ngi-igenomes/test-data/mag/gtdbtk_r202_data.tar.gz"
+    // gtdb_db       = "s3://ngi-igenomes/test-data/mag/gtdbtk_r214_data.tar.gz"
+    skip_gtdbtk   = true
+
+    // TODO TEMPORARY: deactivate SPAdes due to incompatibility of container with fusion file system
+    skip_spades       = true
+    skip_spadeshybrid = true
 
     // reproducibility options for assembly
     spades_fix_cpus       = 10
     spadeshybrid_fix_cpus = 10
     megahit_fix_cpu_1     = true
+
     // available options to enable reproducibility for BUSCO (--busco_db) not used here
     // to allow detection of possible problems in automated lineage selection mode using public databases