include inputs when relabelling (geno and sample files are unchanged)

PGScatalog · Apr 18, 2024 · 7649fff · 7649fff
1 parent 6505818
commit 7649fff
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Showing 2 changed files with 15 additions and 12 deletions.
diff --git a/modules/local/plink2_relabelbim.nf b/modules/local/plink2_relabelbim.nf
@@ -21,9 +21,9 @@ process PLINK2_RELABELBIM {
     tuple val(meta), path(geno), path(variants), path(pheno)
 
     output:
-    tuple val(meta), path("${output}.bed"), emit: geno
-    tuple val(meta), path("${output}.bim.zst"), emit: variants
-    tuple val(meta), path("${output}.fam"), emit: pheno
+    tuple val(meta), path("${output}.bed", includeInputs: true), emit: geno
+    tuple val(meta), path("${output}.bim.zst", includeInputs: false), emit: variants
+    tuple val(meta), path("${output}.fam", includeInputs: true), emit: pheno
     tuple val(meta), path("${output}.vmiss.gz"), emit: vmiss
     path "versions.yml"           , emit: versions
 
@@ -52,9 +52,11 @@ process PLINK2_RELABELBIM {
         --make-just-bim zs \\
         --out ${output}
 
-    # cross platform (mac, linux) method of preserving symlinks
-    cp -a $geno ${output}.bed
-    cp -a $pheno ${output}.fam
+    # -a: cross platform (mac, linux) method of preserving symlinks
+    # || true: if file exists, ignore error, will be handled by includeInputs
+    cp -a $geno ${output}.bed || true
+    cp -a $pheno ${output}.fam || true
+
     gzip ${output}.vmiss
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/local/plink2_relabelpvar.nf b/modules/local/plink2_relabelpvar.nf
@@ -21,9 +21,9 @@ process PLINK2_RELABELPVAR {
     tuple val(meta), path(geno), path(pheno), path(variants)
 
     output:
-    tuple val(meta), path("${output}.pgen"), emit: geno
-    tuple val(meta), path("${output}.pvar.zst") , emit: variants
-    tuple val(meta), path("${output}.psam"), emit: pheno
+    tuple val(meta), path("${output}.pgen", includeInputs: true), emit: geno
+    tuple val(meta), path("${output}.pvar.zst", includeInputs: false) , emit: variants
+    tuple val(meta), path("${output}.psam", includeInputs: true), emit: pheno
     tuple val(meta), path("${output}.vmiss.gz"), emit: vmiss
     path "versions.yml"            , emit: versions
 
@@ -52,9 +52,10 @@ process PLINK2_RELABELPVAR {
         --make-just-pvar zs \\
         --out $output
 
-    # cross platform (mac, linux) method of preserving symlinks
-    cp -a $geno ${output}.pgen
-    cp -a $pheno ${output}.psam
+    # -a: cross platform (mac, linux) method of preserving symlinks
+    # || true: if file exists, ignore error, will be handled by includeInputs
+    cp -a $geno ${output}.pgen || true
+    cp -a $pheno ${output}.psam || true
    
     gzip ${output}.vmiss