Merge branch 'dev' into move-conda-checks

nf-core · Nov 9, 2023 · da06524 · da06524
2 parents 2326b7e + f956dc1
commit da06524
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#655](https://github.com/nf-core/ampliseq/pull/655) - Added `NUMBA_CACHE_DIR` to fix downstream analysis with QIIME2 that failed on some systems
 - [#656](https://github.com/nf-core/ampliseq/pull/656) - Moved conda-check to script-section and replaced `exit 1` with `error()`
 
 ### `Dependencies`

diff --git a/modules/local/qiime2_alphararefaction.nf b/modules/local/qiime2_alphararefaction.nf
@@ -22,7 +22,9 @@ process QIIME2_ALPHARAREFACTION {
         error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     """
-    export XDG_CONFIG_HOME="\${PWD}/HOME"
+    export XDG_CONFIG_HOME="./xdgconfig"
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
 
     maxdepth=\$(count_table_minmax_reads.py $stats maximum 2>&1)
 

diff --git a/modules/local/qiime2_ancom_asv.nf b/modules/local/qiime2_ancom_asv.nf
@@ -23,7 +23,9 @@ process QIIME2_ANCOM_ASV {
         error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     """
-    export XDG_CONFIG_HOME="\${PWD}/HOME"
+    export XDG_CONFIG_HOME="./xdgconfig"
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
 
     qiime composition add-pseudocount \\
         --i-table ${table} \\

diff --git a/modules/local/qiime2_ancom_tax.nf b/modules/local/qiime2_ancom_tax.nf
@@ -21,7 +21,9 @@ process QIIME2_ANCOM_TAX {
         error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     """
-    export XDG_CONFIG_HOME="\${PWD}/HOME"
+    export XDG_CONFIG_HOME="./xdgconfig"
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
     mkdir ancom
 
     # Sum data at the specified level

diff --git a/modules/local/qiime2_barplot.nf b/modules/local/qiime2_barplot.nf
@@ -24,7 +24,9 @@ process QIIME2_BARPLOT {
     suffix = setting ? "_${table.baseName}" : ""
     def metadata_cmd = metadata ? "--m-metadata-file ${metadata}": ""
     """
-    export XDG_CONFIG_HOME="\${PWD}/HOME"
+    export XDG_CONFIG_HOME="./xdgconfig"
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
 
     qiime taxa barplot  \\
         --i-table ${table}  \\

diff --git a/modules/local/qiime2_classify.nf b/modules/local/qiime2_classify.nf
@@ -22,7 +22,9 @@ process QIIME2_CLASSIFY {
         error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     """
-    export XDG_CONFIG_HOME="\${PWD}/HOME"
+    export XDG_CONFIG_HOME="./xdgconfig"
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
 
     qiime feature-classifier classify-sklearn  \\
         --i-classifier ${trained_classifier}  \\

diff --git a/modules/local/qiime2_diversity_adonis.nf b/modules/local/qiime2_diversity_adonis.nf
@@ -21,7 +21,9 @@ process QIIME2_DIVERSITY_ADONIS {
     }
     def args = task.ext.args ?: ''
     """
-    export XDG_CONFIG_HOME="\${PWD}/HOME"
+    export XDG_CONFIG_HOME="./xdgconfig"
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
 
     qiime diversity adonis \\
         --p-n-jobs $task.cpus \\

diff --git a/modules/local/qiime2_diversity_alpha.nf b/modules/local/qiime2_diversity_alpha.nf
@@ -20,7 +20,9 @@ process QIIME2_DIVERSITY_ALPHA {
         error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     """
-    export XDG_CONFIG_HOME="\${PWD}/HOME"
+    export XDG_CONFIG_HOME="./xdgconfig"
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
 
     qiime diversity alpha-group-significance \\
         --i-alpha-diversity ${core} \\

diff --git a/modules/local/qiime2_diversity_beta.nf b/modules/local/qiime2_diversity_beta.nf
@@ -20,7 +20,9 @@ process QIIME2_DIVERSITY_BETA {
         error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     """
-    export XDG_CONFIG_HOME="\${PWD}/HOME"
+    export XDG_CONFIG_HOME="./xdgconfig"
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
 
     qiime diversity beta-group-significance \\
         --i-distance-matrix ${core} \\

diff --git a/modules/local/qiime2_diversity_betaord.nf b/modules/local/qiime2_diversity_betaord.nf
@@ -20,7 +20,9 @@ process QIIME2_DIVERSITY_BETAORD {
         error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     """
-    export XDG_CONFIG_HOME="\${PWD}/HOME"
+    export XDG_CONFIG_HOME="./xdgconfig"
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
     mkdir beta_diversity
 
     qiime emperor plot \\

diff --git a/modules/local/qiime2_diversity_core.nf b/modules/local/qiime2_diversity_core.nf
@@ -30,7 +30,9 @@ process QIIME2_DIVERSITY_CORE {
     # COMMENT: might be fixed in version after QIIME2 2023.5
     export UNIFRAC_USE_GPU=N
 
-    export XDG_CONFIG_HOME="\${PWD}/HOME"
+    export XDG_CONFIG_HOME="./xdgconfig"
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
 
     mindepth=\$(count_table_minmax_reads.py $stats minimum 2>&1)
     if [ \"\$mindepth\" -lt \"$mindepth\" ]; then mindepth=$mindepth; fi

diff --git a/modules/local/qiime2_export_absolute.nf b/modules/local/qiime2_export_absolute.nf
@@ -28,7 +28,9 @@ process QIIME2_EXPORT_ABSOLUTE {
         error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     """
-    export XDG_CONFIG_HOME="\${PWD}/HOME"
+    export XDG_CONFIG_HOME="./xdgconfig"
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
 
     #produce raw count table in biom format "table/feature-table.biom"
     qiime tools export \\

diff --git a/modules/local/qiime2_export_relasv.nf b/modules/local/qiime2_export_relasv.nf
@@ -19,7 +19,9 @@ process QIIME2_EXPORT_RELASV {
         error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     """
-    export XDG_CONFIG_HOME="\${PWD}/HOME"
+    export XDG_CONFIG_HOME="./xdgconfig"
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
 
     #convert to relative abundances
     qiime feature-table relative-frequency \\

diff --git a/modules/local/qiime2_export_reltax.nf b/modules/local/qiime2_export_reltax.nf
@@ -22,7 +22,9 @@ process QIIME2_EXPORT_RELTAX {
         error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     """
-    export XDG_CONFIG_HOME="\${PWD}/HOME"
+    export XDG_CONFIG_HOME="./xdgconfig"
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
 
     ##on several taxa level
     array=(\$(seq ${tax_agglom_min} 1 ${tax_agglom_max}))

diff --git a/modules/local/qiime2_extract.nf b/modules/local/qiime2_extract.nf
@@ -21,7 +21,9 @@ process QIIME2_EXTRACT {
         error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     """
-    export XDG_CONFIG_HOME="\${PWD}/HOME"
+    export XDG_CONFIG_HOME="./xdgconfig"
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
 
     ### Import
     qiime tools import \\

diff --git a/modules/local/qiime2_featuretable_group.nf b/modules/local/qiime2_featuretable_group.nf
@@ -20,7 +20,9 @@ process QIIME2_FEATURETABLE_GROUP {
         error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     """
-    export XDG_CONFIG_HOME="\${PWD}/HOME"
+    export XDG_CONFIG_HOME="./xdgconfig"
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
 
     qiime feature-table filter-samples \\
         --i-table "${table}" \\

diff --git a/modules/local/qiime2_filtersamples.nf b/modules/local/qiime2_filtersamples.nf
@@ -22,7 +22,9 @@ process QIIME2_FILTERSAMPLES {
     def args = task.ext.args ?: "--p-where \'${filter}<>\"\"\'"
     def prefix = task.ext.prefix ?: "${filter}"
     """
-    export XDG_CONFIG_HOME="\${PWD}/HOME"
+    export XDG_CONFIG_HOME="./xdgconfig"
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
 
     qiime feature-table filter-samples \\
         --i-table ${table} \\

diff --git a/modules/local/qiime2_filtertaxa.nf b/modules/local/qiime2_filtertaxa.nf
@@ -27,7 +27,9 @@ process QIIME2_FILTERTAXA {
         error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     """
-    export XDG_CONFIG_HOME="\${PWD}/HOME"
+    export XDG_CONFIG_HOME="./xdgconfig"
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
 
     if ! [ \"${exclude_taxa}\" = \"none\" ]; then
         #filter sequences

diff --git a/modules/local/qiime2_inasv.nf b/modules/local/qiime2_inasv.nf
@@ -20,6 +20,9 @@ process QIIME2_INASV {
         error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     """
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
+
     # remove first line if needed
     sed '/^# Constructed from biom file/d' "$asv" > biom-table.txt
 

diff --git a/modules/local/qiime2_inseq.nf b/modules/local/qiime2_inseq.nf
@@ -20,6 +20,9 @@ process QIIME2_INSEQ {
         error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     """
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
+
     qiime tools import \\
         --input-path "$seq" \\
         --type 'FeatureData[Sequence]' \\

diff --git a/modules/local/qiime2_intax.nf b/modules/local/qiime2_intax.nf
@@ -22,6 +22,9 @@ process QIIME2_INTAX {
     }
     def script_cmd = script ? "$script $tax" : "cp $tax tax.tsv"
     """
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
+
     $script_cmd
 
     qiime tools import \\

diff --git a/modules/local/qiime2_intree.nf b/modules/local/qiime2_intree.nf
@@ -20,6 +20,9 @@ process QIIME2_INTREE {
         error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     """
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
+
     qiime tools import \\
         --type 'Phylogeny[Rooted]' \\
         --input-path $tree \\

diff --git a/modules/local/qiime2_train.nf b/modules/local/qiime2_train.nf
@@ -21,7 +21,9 @@ process QIIME2_TRAIN {
         error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     """
-    export XDG_CONFIG_HOME="\${PWD}/HOME"
+    export XDG_CONFIG_HOME="./xdgconfig"
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
 
     #Train classifier
     qiime feature-classifier fit-classifier-naive-bayes \\

diff --git a/modules/local/qiime2_tree.nf b/modules/local/qiime2_tree.nf
@@ -20,7 +20,9 @@ process QIIME2_TREE {
         error "QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     """
-    export XDG_CONFIG_HOME="\${PWD}/HOME"
+    export XDG_CONFIG_HOME="./xdgconfig"
+    export MPLCONFIGDIR="./mplconfigdir"
+    export NUMBA_CACHE_DIR="./numbacache"
 
     qiime alignment mafft \\
         --i-sequences ${repseq} \\

diff --git a/subworkflows/local/dada2_taxonomy_wf.nf b/subworkflows/local/dada2_taxonomy_wf.nf
@@ -83,7 +83,7 @@ workflow DADA2_TAXONOMY_WF {
         //set file name prefix for SH assignments
         if (!params.skip_dada_addspecies) {
             ASV_SH_name = "ASV_tax_species_SH"
-	} else {
+    } else {
             ASV_SH_name = "ASV_tax_SH"
         }
         //find SHs