diff --git a/bin/collect_genotypes.py b/bin/collect_genotypes.py
index 6746f499a..34a35c416 100755
--- a/bin/collect_genotypes.py
+++ b/bin/collect_genotypes.py
@@ -50,7 +50,7 @@ def validate_eigenstrat(genof, snpf, indf):
 
 VERSION = "1.0.0"
 
-parser = argparse.ArgumentParser(usage="%(prog)s (-i <Input file prefix>) (-c <input ind file> | -R | -E) [-L <SAMPLE LIST> | -S Ind [-S Ind2]] [-o <OUTPUT FILE PREFIX>]" , description="A tool to check two different EingenStrat databses for shared individuals, and extract or remove individuals from an EigenStrat database.")
+parser = argparse.ArgumentParser(usage="%(prog)s [-v] (-g1 <GENO FILE 1 NAME>) (-s1 <SNP FILE 1 NAME>) (-i1 <IND FILE 1 NAME>) (-g2 <GENO FILE 2 NAME>) (-s2 <SNP FILE 2 NAME>) (-i2 <IND FILE 2 NAME>) (-o <OUTPUT FILE PREFIX>)" , description="A tool to put together two EIGENSTRAT datasets of genotyped on the same SNP set into a single dataset.")
 parser._optionals.title = "Available options"
 parser.add_argument("-g1", "--genoFn1", type = str, metavar = "<GENO FILE 1 NAME>",    required = True, help = "The path to the input geno file of the first dataset.")
 parser.add_argument("-s1", "--snpFn1",  type = str, metavar = "<SNP FILE 1 NAME>",     required = True, help = "The path to the input snp file of the first dataset.")
diff --git a/subworkflows/local/map.nf b/subworkflows/local/map.nf
index 10972a2a7..cbd4e20f9 100644
--- a/subworkflows/local/map.nf
+++ b/subworkflows/local/map.nf
@@ -66,7 +66,7 @@ workflow MAP {
 
     if ( params.mapping_tool == 'bwaaln' ) {
         ch_index_for_mapping = index.map{ meta, index, fasta -> [ meta, index ] }
-        ch_reads_for_mapping = reads
+        ch_reads_for_mapping = ch_input_for_mapping.reads
 
         FASTQ_ALIGN_BWAALN ( ch_reads_for_mapping, ch_index_for_mapping )
         ch_versions        = ch_versions.mix ( FASTQ_ALIGN_BWAALN.out.versions.first() )
@@ -81,7 +81,7 @@ workflow MAP {
         ch_mapped_lane_bai = params.fasta_largeref ? FASTQ_ALIGN_BWAALN.out.csi : FASTQ_ALIGN_BWAALN.out.bai
 
     } else if ( params.mapping_tool == 'bwamem' ) {
-        ch_input_for_mapping = reads
+        ch_input_for_mapping = ch_input_for_mapping.reads
                             .combine( index )
                             .multiMap {
                                 meta, reads, meta2, index, fasta ->
@@ -100,7 +100,7 @@ workflow MAP {
         ch_mapped_lane_bai = params.fasta_largeref ? SAMTOOLS_INDEX_MEM.out.csi : SAMTOOLS_INDEX_MEM.out.bai
 
     } else if ( params.mapping_tool == 'bowtie2' ) {
-        ch_input_for_mapping = reads
+        ch_input_for_mapping = ch_input_for_mapping.reads
                             .combine( index.map{ meta, index, fasta -> [ meta, index ] } )
                             .multiMap {
                                 meta, reads, meta2, index ->
@@ -124,7 +124,7 @@ workflow MAP {
                                 [ meta, elongated_index ]
                                 }
 
-        CIRCULARMAPPER( index, ch_elongated_reference_for_mapping, elongated_chr_list, reads, params.fasta_circularmapper_elongationfactor )
+        CIRCULARMAPPER( index, ch_elongated_reference_for_mapping, elongated_chr_list, ch_input_for_mapping.reads, params.fasta_circularmapper_elongationfactor )
         ch_versions        = ch_versions.mix ( CIRCULARMAPPER.out.versions )
         ch_mapped_lane_bam      = CIRCULARMAPPER.out.bam
         ch_mapped_lane_bai      = CIRCULARMAPPER.out.bai // [ [ meta ], bai/csi ]