replace tab with 4 spaces

nf-core · Nov 7, 2023 · ac8b05c · ac8b05c
1 parent b6b7928
commit ac8b05c
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Showing 20 changed files with 20 additions and 20 deletions.
diff --git a/modules/local/qiime2_alphararefaction.nf b/modules/local/qiime2_alphararefaction.nf
@@ -24,7 +24,7 @@ process QIIME2_ALPHARAREFACTION {
     script:
     """
     export XDG_CONFIG_HOME="./xdgconfig"
-	export MPLCONFIGDIR="./mplconfigdir"
+    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
@@ -25,7 +25,7 @@ process QIIME2_ANCOM_ASV {
     script:
     """
     export XDG_CONFIG_HOME="./xdgconfig"
-	export MPLCONFIGDIR="./mplconfigdir"
+    export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
 
     qiime composition add-pseudocount \\

diff --git a/modules/local/qiime2_ancom_tax.nf b/modules/local/qiime2_ancom_tax.nf
@@ -23,7 +23,7 @@ process QIIME2_ANCOM_TAX {
     script:
     """
     export XDG_CONFIG_HOME="./xdgconfig"
-	export MPLCONFIGDIR="./mplconfigdir"
+    export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
     mkdir ancom
 

diff --git a/modules/local/qiime2_barplot.nf b/modules/local/qiime2_barplot.nf
@@ -26,7 +26,7 @@ process QIIME2_BARPLOT {
     def metadata_cmd = metadata ? "--m-metadata-file ${metadata}": ""
     """
     export XDG_CONFIG_HOME="./xdgconfig"
-	export MPLCONFIGDIR="./mplconfigdir"
+    export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
 
     qiime taxa barplot  \\

diff --git a/modules/local/qiime2_classify.nf b/modules/local/qiime2_classify.nf
@@ -24,7 +24,7 @@ process QIIME2_CLASSIFY {
     script:
     """
     export XDG_CONFIG_HOME="./xdgconfig"
-	export MPLCONFIGDIR="./mplconfigdir"
+    export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
 
     qiime feature-classifier classify-sklearn  \\

diff --git a/modules/local/qiime2_diversity_adonis.nf b/modules/local/qiime2_diversity_adonis.nf
@@ -23,7 +23,7 @@ process QIIME2_DIVERSITY_ADONIS {
     def args = task.ext.args ?: ''
     """
     export XDG_CONFIG_HOME="./xdgconfig"
-	export MPLCONFIGDIR="./mplconfigdir"
+    export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
 
     qiime diversity adonis \\

diff --git a/modules/local/qiime2_diversity_alpha.nf b/modules/local/qiime2_diversity_alpha.nf
@@ -22,7 +22,7 @@ process QIIME2_DIVERSITY_ALPHA {
     script:
     """
     export XDG_CONFIG_HOME="./xdgconfig"
-	export MPLCONFIGDIR="./mplconfigdir"
+    export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
 
     qiime diversity alpha-group-significance \\

diff --git a/modules/local/qiime2_diversity_beta.nf b/modules/local/qiime2_diversity_beta.nf
@@ -22,7 +22,7 @@ process QIIME2_DIVERSITY_BETA {
     script:
     """
     export XDG_CONFIG_HOME="./xdgconfig"
-	export MPLCONFIGDIR="./mplconfigdir"
+    export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
 
     qiime diversity beta-group-significance \\

diff --git a/modules/local/qiime2_diversity_betaord.nf b/modules/local/qiime2_diversity_betaord.nf
@@ -22,7 +22,7 @@ process QIIME2_DIVERSITY_BETAORD {
     script:
     """
     export XDG_CONFIG_HOME="./xdgconfig"
-	export MPLCONFIGDIR="./mplconfigdir"
+    export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
     mkdir beta_diversity
 

diff --git a/modules/local/qiime2_diversity_core.nf b/modules/local/qiime2_diversity_core.nf
@@ -32,7 +32,7 @@ process QIIME2_DIVERSITY_CORE {
     export UNIFRAC_USE_GPU=N
 
     export XDG_CONFIG_HOME="./xdgconfig"
-	export MPLCONFIGDIR="./mplconfigdir"
+    export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
 
     mindepth=\$(count_table_minmax_reads.py $stats minimum 2>&1)

diff --git a/modules/local/qiime2_export_absolute.nf b/modules/local/qiime2_export_absolute.nf
@@ -30,7 +30,7 @@ process QIIME2_EXPORT_ABSOLUTE {
     script:
     """
     export XDG_CONFIG_HOME="./xdgconfig"
-	export MPLCONFIGDIR="./mplconfigdir"
+    export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
 
     #produce raw count table in biom format "table/feature-table.biom"

diff --git a/modules/local/qiime2_export_relasv.nf b/modules/local/qiime2_export_relasv.nf
@@ -21,7 +21,7 @@ process QIIME2_EXPORT_RELASV {
     script:
     """
     export XDG_CONFIG_HOME="./xdgconfig"
-	export MPLCONFIGDIR="./mplconfigdir"
+    export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
 
     #convert to relative abundances

diff --git a/modules/local/qiime2_export_reltax.nf b/modules/local/qiime2_export_reltax.nf
@@ -24,7 +24,7 @@ process QIIME2_EXPORT_RELTAX {
     script:
     """
     export XDG_CONFIG_HOME="./xdgconfig"
-	export MPLCONFIGDIR="./mplconfigdir"
+    export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
 
     ##on several taxa level

diff --git a/modules/local/qiime2_extract.nf b/modules/local/qiime2_extract.nf
@@ -23,7 +23,7 @@ process QIIME2_EXTRACT {
     script:
     """
     export XDG_CONFIG_HOME="./xdgconfig"
-	export MPLCONFIGDIR="./mplconfigdir"
+    export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
 
     ### Import

diff --git a/modules/local/qiime2_featuretable_group.nf b/modules/local/qiime2_featuretable_group.nf
@@ -22,7 +22,7 @@ process QIIME2_FEATURETABLE_GROUP {
     script:
     """
     export XDG_CONFIG_HOME="./xdgconfig"
-	export MPLCONFIGDIR="./mplconfigdir"
+    export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
 
     qiime feature-table filter-samples \\

diff --git a/modules/local/qiime2_filtersamples.nf b/modules/local/qiime2_filtersamples.nf
@@ -24,7 +24,7 @@ process QIIME2_FILTERSAMPLES {
     def prefix = task.ext.prefix ?: "${filter}"
     """
     export XDG_CONFIG_HOME="./xdgconfig"
-	export MPLCONFIGDIR="./mplconfigdir"
+    export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
 
     qiime feature-table filter-samples \\

diff --git a/modules/local/qiime2_filtertaxa.nf b/modules/local/qiime2_filtertaxa.nf
@@ -29,7 +29,7 @@ process QIIME2_FILTERTAXA {
     script:
     """
     export XDG_CONFIG_HOME="./xdgconfig"
-	export MPLCONFIGDIR="./mplconfigdir"
+    export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
 
     if ! [ \"${exclude_taxa}\" = \"none\" ]; then

diff --git a/modules/local/qiime2_train.nf b/modules/local/qiime2_train.nf
@@ -23,7 +23,7 @@ process QIIME2_TRAIN {
     script:
     """
     export XDG_CONFIG_HOME="./xdgconfig"
-	export MPLCONFIGDIR="./mplconfigdir"
+    export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
 
     #Train classifier

diff --git a/modules/local/qiime2_tree.nf b/modules/local/qiime2_tree.nf
@@ -22,7 +22,7 @@ process QIIME2_TREE {
     script:
     """
     export XDG_CONFIG_HOME="./xdgconfig"
-	export MPLCONFIGDIR="./mplconfigdir"
+    export MPLCONFIGDIR="./mplconfigdir"
     export NUMBA_CACHE_DIR="./numbacache"
 
     qiime alignment mafft \\

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