From 83a9e2a8c6f0ae79a6b2eded1e70dc6b5bfee28f Mon Sep 17 00:00:00 2001
From: Victoria Carr <vc11@sanger.ac.uk>
Date: Tue, 16 Aug 2022 14:06:50 +0100
Subject: [PATCH 1/5] Remove intermediate files

---
 main.nf                   |  4 ----
 modules/mlst.nf           | 12 ++++++------
 modules/pbp_typer.nf      |  4 ++++
 modules/res_alignments.nf | 12 +++++++++---
 modules/res_typer.nf      |  2 +-
 modules/serotyping.nf     |  2 +-
 modules/surface_typer.nf  |  3 ++-
 7 files changed, 23 insertions(+), 16 deletions(-)

diff --git a/main.nf b/main.nf
index f53c4c1..cb7d6e7 100644
--- a/main.nf
+++ b/main.nf
@@ -189,14 +189,12 @@ workflow MLST {
         // Collect outputs
         new_alleles = get_mlst_allele_and_pileup.out.new_alleles
         pileup = get_mlst_allele_and_pileup.out.pileup
-        existing_alleles = get_mlst_allele_and_pileup.out.existing_alleles
         status = get_mlst_allele_and_pileup.out.new_alleles_status
         srst2_results = srst2_for_mlst.out.srst2_results
 
     emit:
         new_alleles
         pileup
-        existing_alleles
         status
         srst2_results
 }
@@ -325,8 +323,6 @@ workflow {
             MLST.out.pileup.subscribe { it ->
                 it.copyTo(file("${results_dir}"))
             }
-            MLST.out.existing_alleles
-                .collectFile(name: file("${results_dir}/${params.existing_mlst_alleles_out}"), keepHeader: true, sort: true)
             MLST.out.status
                 .collectFile(name: file("${results_dir}/${params.new_mlst_alleles_status}"), keepHeader: false, sort: true)
 
diff --git a/modules/mlst.nf b/modules/mlst.nf
index 84008d7..1a3f297 100644
--- a/modules/mlst.nf
+++ b/modules/mlst.nf
@@ -15,10 +15,12 @@ process srst2_for_mlst {
     mlst_name="Streptococcus_agalactiae"
 
     """
-    set +e
+
     getmlst.py --species 'Streptococcus agalactiae'
     srst2 --samtools_args '\\-A' --input_pe ${reads[0]} ${reads[1]} --output ${pair_id} --save_scores --mlst_db ${mlst_db} --mlst_definitions profiles_csv --mlst_delimiter '_' --min_coverage ${min_coverage}
+
     touch ${pair_id}__mlst__${mlst_name}__results.txt
+    find . \\! -type f \\( -name "${pair_id}*.bam" -o -name "${pair_id}__mlst__${mlst_name}__results.txt" -o -name ${mlst_db} \\) -delete
     """
 }
 
@@ -31,17 +33,15 @@ process get_mlst_allele_and_pileup {
     output:
     path(output_new_mlst_alleles_fasta), emit: new_alleles, optional: true
     path(output_new_mlst_pileup), emit: pileup, optional: true
-    path(output_existing_mlst_alleles), emit: existing_alleles, optional: true
     path(output_new_mlst_alleles_log), emit: new_alleles_status
 
     script:
     output_new_mlst_alleles_fasta="${pair_id}_new_mlst_alleles.fasta"
     output_new_mlst_pileup="${pair_id}_new_mlst_pileup.txt"
-    output_existing_mlst_alleles="${pair_id}_existing_mlst_alleles.txt"
     output_new_mlst_alleles_log="${pair_id}_new_mlst_alleles.log"
 
     """
-    set +e
+
     # Get alleles from mismatches in SRST2 MLST results file
     samtools index ${bam_file}
     get_alleles_from_srst2_mlst.py --mlst_results_file ${results_file} --min_read_depth ${min_read_depth} --output_prefix ${pair_id}
@@ -81,11 +81,11 @@ process get_mlst_allele_and_pileup {
         echo "${pair_id}: No new MLST alleles found." > tmp.log
     fi
 
-
-    touch ${pair_id}_new_mlst_alleles.log
     mv tmp.fasta ${output_new_mlst_alleles_fasta}
     mv tmp_pileup.txt ${output_new_mlst_pileup}
     mv tmp.log ${output_new_mlst_alleles_log}
+
+    find . \\! -type f \\( -name "${pair_id}_new_mlst_alleles.log" -o -name ${output_new_mlst_alleles_fasta} -o -name ${output_new_mlst_pileup} \\) -delete
     """
 
 }
diff --git a/modules/pbp_typer.nf b/modules/pbp_typer.nf
index 6ffb353..8eca3c2 100644
--- a/modules/pbp_typer.nf
+++ b/modules/pbp_typer.nf
@@ -17,6 +17,8 @@ process get_pbp_genes {
 
     # Get BED file of PBP fragments
     get_pbp_genes_from_contigs.py --blast_out_file ${pair_id}_blast_blactam.out --query_fasta ${blactam_ref} --frac_align_len_threshold ${frac_align_len_threshold} --frac_identity_threshold ${frac_identity_len_threshold} --output_prefix ${pair_id}_
+
+    find . \\! -type f \\( -name "${pair_id}_*bed" -o -name ${contigs} \\) -delete
     """
 }
 
@@ -46,5 +48,7 @@ process get_pbp_alleles {
         # Get identical or imperfect hits
         get_pbp_alleles.py --blast_out_file ${pair_id}_blast_${pbp_type}.out --query_fasta ${pair_id}_${pbp_type}.faa --output_prefix ${pair_id}_${pbp_type}_PBP
     fi
+
+    find . \\! -type f \\( -name "${pair_id}_${pbp_type}_PBP_new_allele.faa" -o -name "${pair_id}_${pbp_type}_PBP_existing_allele.txt" \\) -delete
     """
 }
diff --git a/modules/res_alignments.nf b/modules/res_alignments.nf
index cd25cef..d9bc362 100644
--- a/modules/res_alignments.nf
+++ b/modules/res_alignments.nf
@@ -13,9 +13,11 @@ process srst2_for_res_typing {
     script:
     db_name=db.getSimpleName()
     """
-    set +e
+
     srst2 --samtools_args '\\-A' --input_pe ${reads[0]} ${reads[1]} --output ${pair_id} --log --save_scores --min_coverage ${min_coverage} --max_divergence ${max_divergence} --gene_db ${db}
+
     touch ${pair_id}__fullgenes__${db_name}__results.txt
+    find . \\! -type f \\( -name "${pair_id}*.bam" -o -name "${pair_id}__fullgenes__${db_name}__results.txt" \\) -delete
     """
 }
 
@@ -45,15 +47,17 @@ process split_target_RES_seq_from_sam_file {
     file("*_*_${pair_id}*.bai")
 
     """
-    set +e
+
     samtools view -h ${bam_file} > \$(basename ${bam_file} .bam).sam
     get_targets_from_samfile.py -s \$(basename ${bam_file} .bam).sam -t ${targets_file} -i ${pair_id} -o CHECK_
     for check_sam_file in CHECK_*_${pair_id}*.sam; do
         samtools view -bS \${check_sam_file} > \$(basename \${check_sam_file} .sam).bam
         samtools index \$(basename \${check_sam_file} .sam).bam \$(basename \${check_sam_file} .sam).bai
     done
+
     touch dummy_dummy_${pair_id}_dummy.bam
     touch dummy_dummy_${pair_id}_dummy.bai
+    find . \\! -type f \\( -name "*_*_${pair_id}*.bam" -o -name "*_*_${pair_id}*.bai" \\) -delete
     """
 }
 
@@ -69,7 +73,7 @@ process freebayes {
     tuple val(pair_id), file("${pair_id}_consensus_seq.fna"), emit: consensus
 
     """
-    set +e
+
     for check_bam_file in CHECK_*_${pair_id}*.bam; do
         target=\$(echo \${check_bam_file} | sed 's/CHECK_//g' | sed 's/_${pair_id}.*//g')
         freebayes -q 20 -p 1 -f CHECK_\${target}_ref.fna \${check_bam_file} -v CHECK_\${target}_${pair_id}_seq.vcf
@@ -77,6 +81,8 @@ process freebayes {
         tabix -p vcf CHECK_\${target}_${pair_id}_seq.vcf.gz
         cat CHECK_\${target}_ref.fna | vcf-consensus CHECK_\${target}_${pair_id}_seq.vcf.gz >> ${pair_id}_consensus_seq.fna
     done
+
     touch ${pair_id}_consensus_seq.fna
+    find . \\! -name "${pair_id}_consensus_seq.fna" -delete
     """
 }
diff --git a/modules/res_typer.nf b/modules/res_typer.nf
index a0c8edc..d499e37 100644
--- a/modules/res_typer.nf
+++ b/modules/res_typer.nf
@@ -15,7 +15,7 @@ process res_typer {
     variants_output_file="${pair_id}_res_gbs_variants.txt"
     alleles_accessions_file="${pair_id}_res_alleles_accessions.txt"
     """
-    set +e
+
     process_res_typer_results.py \
         --srst2_gbs_fullgenes ${gbs_fullgenes} \
         --srst2_gbs_consensus ${gbs_consensus} \
diff --git a/modules/serotyping.nf b/modules/serotyping.nf
index 7458a6f..a2abac3 100644
--- a/modules/serotyping.nf
+++ b/modules/serotyping.nf
@@ -12,7 +12,6 @@ process serotyping {
     sero_gene_db="GBS-SBG.fasta"
 
     """
-    set +e
 
     # Get latest version of GBS Serotype Database
     git clone https://github.com/swainechen/GBS-SBG
@@ -22,5 +21,6 @@ process serotyping {
     process_serotyper_results.py --srst2_output SERO_${pair_id} --sero_db ${sero_gene_db} --output ${pair_id}_SeroType_Results.txt --min_read_depth ${min_read_depth}
 
     touch ${output_file}
+    find . \\! -name ${output_file} -delete
     """
 }
diff --git a/modules/surface_typer.nf b/modules/surface_typer.nf
index 64a48ff..7230898 100644
--- a/modules/surface_typer.nf
+++ b/modules/surface_typer.nf
@@ -14,11 +14,12 @@ process surface_typer {
     inc_output_file="${pair_id}_surface_protein_incidence_sample.txt"
     variants_output_file="${pair_id}_surface_protein_variants_sample.txt"
     """
-    set +e
+
     srst2 --samtools_args '\\-A' --input_pe ${reads[0]} ${reads[1]} --output ${pair_id}_SURFACE --log --save_scores --min_coverage ${min_coverage} --max_divergence ${max_divergence} --gene_db ${surface_protein_db}
     process_surface_typer_results.py --srst2_gbs_fullgenes ${pair_id}_SURFACE --surface_db ${surface_protein_db} --output_prefix ${pair_id} --min_read_depth ${min_read_depth}
 
     touch ${inc_output_file}
     touch ${variants_output_file}
+    find . \\! -type f \\( -name ${inc_output_file} -o -name ${variants_output_file} \\) -delete
     """
 }

From b5fd9a1d7553eac9c3f1f7eac26dbf16514cb58e Mon Sep 17 00:00:00 2001
From: Victoria Carr <vc11@sanger.ac.uk>
Date: Tue, 16 Aug 2022 14:28:02 +0100
Subject: [PATCH 2/5] Fix missing mlst outputs

---
 modules/mlst.nf | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/modules/mlst.nf b/modules/mlst.nf
index 1a3f297..3fee020 100644
--- a/modules/mlst.nf
+++ b/modules/mlst.nf
@@ -81,8 +81,16 @@ process get_mlst_allele_and_pileup {
         echo "${pair_id}: No new MLST alleles found." > tmp.log
     fi
 
-    mv tmp.fasta ${output_new_mlst_alleles_fasta}
-    mv tmp_pileup.txt ${output_new_mlst_pileup}
+    if [ -f tmp.fasta ]
+    then
+        mv tmp.fasta ${output_new_mlst_alleles_fasta}
+    fi
+
+    if [ -f tmp_pileup.txt ]
+    then
+        mv tmp_pileup.txt ${output_new_mlst_pileup}
+    fi
+    
     mv tmp.log ${output_new_mlst_alleles_log}
 
     find . \\! -type f \\( -name "${pair_id}_new_mlst_alleles.log" -o -name ${output_new_mlst_alleles_fasta} -o -name ${output_new_mlst_pileup} \\) -delete

From 6f5aa1464d658f58748a05880c6955e07ed74a8d Mon Sep 17 00:00:00 2001
From: Victoria Carr <vc11@sanger.ac.uk>
Date: Tue, 16 Aug 2022 14:34:21 +0100
Subject: [PATCH 3/5] Remove delete files in pbp typer

---
 modules/pbp_typer.nf | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/modules/pbp_typer.nf b/modules/pbp_typer.nf
index 8eca3c2..6ffb353 100644
--- a/modules/pbp_typer.nf
+++ b/modules/pbp_typer.nf
@@ -17,8 +17,6 @@ process get_pbp_genes {
 
     # Get BED file of PBP fragments
     get_pbp_genes_from_contigs.py --blast_out_file ${pair_id}_blast_blactam.out --query_fasta ${blactam_ref} --frac_align_len_threshold ${frac_align_len_threshold} --frac_identity_threshold ${frac_identity_len_threshold} --output_prefix ${pair_id}_
-
-    find . \\! -type f \\( -name "${pair_id}_*bed" -o -name ${contigs} \\) -delete
     """
 }
 
@@ -48,7 +46,5 @@ process get_pbp_alleles {
         # Get identical or imperfect hits
         get_pbp_alleles.py --blast_out_file ${pair_id}_blast_${pbp_type}.out --query_fasta ${pair_id}_${pbp_type}.faa --output_prefix ${pair_id}_${pbp_type}_PBP
     fi
-
-    find . \\! -type f \\( -name "${pair_id}_${pbp_type}_PBP_new_allele.faa" -o -name "${pair_id}_${pbp_type}_PBP_existing_allele.txt" \\) -delete
     """
 }

From b236b47bd7fa580293aae050a49daae6aa1477e1 Mon Sep 17 00:00:00 2001
From: Victoria Carr <vc11@sanger.ac.uk>
Date: Tue, 16 Aug 2022 14:56:17 +0100
Subject: [PATCH 4/5] Undo remove optional existing alleles file

---
 main.nf         | 4 ++++
 modules/mlst.nf | 4 +++-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index cb7d6e7..f53c4c1 100644
--- a/main.nf
+++ b/main.nf
@@ -189,12 +189,14 @@ workflow MLST {
         // Collect outputs
         new_alleles = get_mlst_allele_and_pileup.out.new_alleles
         pileup = get_mlst_allele_and_pileup.out.pileup
+        existing_alleles = get_mlst_allele_and_pileup.out.existing_alleles
         status = get_mlst_allele_and_pileup.out.new_alleles_status
         srst2_results = srst2_for_mlst.out.srst2_results
 
     emit:
         new_alleles
         pileup
+        existing_alleles
         status
         srst2_results
 }
@@ -323,6 +325,8 @@ workflow {
             MLST.out.pileup.subscribe { it ->
                 it.copyTo(file("${results_dir}"))
             }
+            MLST.out.existing_alleles
+                .collectFile(name: file("${results_dir}/${params.existing_mlst_alleles_out}"), keepHeader: true, sort: true)
             MLST.out.status
                 .collectFile(name: file("${results_dir}/${params.new_mlst_alleles_status}"), keepHeader: false, sort: true)
 
diff --git a/modules/mlst.nf b/modules/mlst.nf
index 3fee020..e3d39e6 100644
--- a/modules/mlst.nf
+++ b/modules/mlst.nf
@@ -33,11 +33,13 @@ process get_mlst_allele_and_pileup {
     output:
     path(output_new_mlst_alleles_fasta), emit: new_alleles, optional: true
     path(output_new_mlst_pileup), emit: pileup, optional: true
+    path(output_existing_mlst_alleles), emit: existing_alleles, optional: true
     path(output_new_mlst_alleles_log), emit: new_alleles_status
 
     script:
     output_new_mlst_alleles_fasta="${pair_id}_new_mlst_alleles.fasta"
     output_new_mlst_pileup="${pair_id}_new_mlst_pileup.txt"
+    output_existing_mlst_alleles="${pair_id}_existing_mlst_alleles.txt"
     output_new_mlst_alleles_log="${pair_id}_new_mlst_alleles.log"
 
     """
@@ -90,7 +92,7 @@ process get_mlst_allele_and_pileup {
     then
         mv tmp_pileup.txt ${output_new_mlst_pileup}
     fi
-    
+
     mv tmp.log ${output_new_mlst_alleles_log}
 
     find . \\! -type f \\( -name "${pair_id}_new_mlst_alleles.log" -o -name ${output_new_mlst_alleles_fasta} -o -name ${output_new_mlst_pileup} \\) -delete

From c0d2d3e3174308320d4769560425dd66ef926cdc Mon Sep 17 00:00:00 2001
From: Victoria Carr <vc11@sanger.ac.uk>
Date: Wed, 17 Aug 2022 16:34:58 +0100
Subject: [PATCH 5/5] Unlink and remove unnecessary files

---
 modules/combine.nf        |  9 +++++++++
 modules/mlst.nf           | 19 ++++++++++++++++--
 modules/pbp_typer.nf      | 15 ++++++++++++++
 modules/res_alignments.nf | 41 +++++++++++++++++++++++++++++++++++----
 modules/serotyping.nf     | 10 +++++++++-
 modules/surface_typer.nf  | 11 ++++++++++-
 6 files changed, 97 insertions(+), 8 deletions(-)

diff --git a/modules/combine.nf b/modules/combine.nf
index e9f908d..6bac8d1 100644
--- a/modules/combine.nf
+++ b/modules/combine.nf
@@ -19,6 +19,15 @@ process combine_results {
         -x "${surface_protein_incidence}" \
         -n "${version}" \
         -o ${pair_id}
+
+    unlink ${sero_results}
+    unlink ${res_incidence}
+    unlink ${res_alleles}
+    unlink ${surface_protein_incidence}
+    unlink ${surface_protein_variants}
+    unlink ${mlst_allelic_frequency}
+    unlink ${version}
+    unlink ${config}
     """
 }
 
diff --git a/modules/mlst.nf b/modules/mlst.nf
index e3d39e6..cb3d68b 100644
--- a/modules/mlst.nf
+++ b/modules/mlst.nf
@@ -20,7 +20,19 @@ process srst2_for_mlst {
     srst2 --samtools_args '\\-A' --input_pe ${reads[0]} ${reads[1]} --output ${pair_id} --save_scores --mlst_db ${mlst_db} --mlst_definitions profiles_csv --mlst_delimiter '_' --min_coverage ${min_coverage}
 
     touch ${pair_id}__mlst__${mlst_name}__results.txt
-    find . \\! -type f \\( -name "${pair_id}*.bam" -o -name "${pair_id}__mlst__${mlst_name}__results.txt" -o -name ${mlst_db} \\) -delete
+
+    # Clean directory
+    mkdir output
+    mv ${pair_id}*.bam output
+    mv ${pair_id}__mlst__${mlst_name}__results.txt output
+    mv ${mlst_db} output
+    find . -maxdepth 1 -type f -delete
+    unlink ${reads[0]}
+    unlink ${reads[1]}
+    mv output/${pair_id}*.bam .
+    mv output/${pair_id}__mlst__${mlst_name}__results.txt .
+    mv output/${mlst_db} .
+    rm -d output
     """
 }
 
@@ -95,7 +107,10 @@ process get_mlst_allele_and_pileup {
 
     mv tmp.log ${output_new_mlst_alleles_log}
 
-    find . \\! -type f \\( -name "${pair_id}_new_mlst_alleles.log" -o -name ${output_new_mlst_alleles_fasta} -o -name ${output_new_mlst_pileup} \\) -delete
+    # Clean
+    unlink ${bam_file}
+    unlink ${results_file}
+    unlink ${mlst_alleles}
     """
 
 }
diff --git a/modules/pbp_typer.nf b/modules/pbp_typer.nf
index 6ffb353..8839f4c 100644
--- a/modules/pbp_typer.nf
+++ b/modules/pbp_typer.nf
@@ -17,6 +17,16 @@ process get_pbp_genes {
 
     # Get BED file of PBP fragments
     get_pbp_genes_from_contigs.py --blast_out_file ${pair_id}_blast_blactam.out --query_fasta ${blactam_ref} --frac_align_len_threshold ${frac_align_len_threshold} --frac_identity_threshold ${frac_identity_len_threshold} --output_prefix ${pair_id}_
+
+    # Clean directory
+    mkdir output
+    mv ${pair_id}_*bed output
+    mv ${contigs} output
+    find . -maxdepth 1 -type f -delete
+    unlink ${blactam_ref}
+    mv output/${pair_id}_*bed .
+    mv output/${contigs} .
+    rm -d output
     """
 }
 
@@ -45,6 +55,11 @@ process get_pbp_alleles {
 
         # Get identical or imperfect hits
         get_pbp_alleles.py --blast_out_file ${pair_id}_blast_${pbp_type}.out --query_fasta ${pair_id}_${pbp_type}.faa --output_prefix ${pair_id}_${pbp_type}_PBP
+
+        unlink ${pair_id}_${pbp_type}.bed
     fi
+
+    unlink ${contigs}
+    unlink ${gbs_blactam_db}
     """
 }
diff --git a/modules/res_alignments.nf b/modules/res_alignments.nf
index d9bc362..1296753 100644
--- a/modules/res_alignments.nf
+++ b/modules/res_alignments.nf
@@ -17,7 +17,18 @@ process srst2_for_res_typing {
     srst2 --samtools_args '\\-A' --input_pe ${reads[0]} ${reads[1]} --output ${pair_id} --log --save_scores --min_coverage ${min_coverage} --max_divergence ${max_divergence} --gene_db ${db}
 
     touch ${pair_id}__fullgenes__${db_name}__results.txt
-    find . \\! -type f \\( -name "${pair_id}*.bam" -o -name "${pair_id}__fullgenes__${db_name}__results.txt" \\) -delete
+
+    # Clean directory
+    mkdir output
+    mv ${pair_id}*.bam output
+    mv ${pair_id}__fullgenes__${db_name}__results.txt output
+    find . -maxdepth 1 -type f -delete
+    unlink ${reads[0]}
+    unlink ${reads[1]}
+    unlink ${db}
+    mv output/${pair_id}*.bam .
+    mv output/${pair_id}__fullgenes__${db_name}__results.txt .
+    rm -d output
     """
 }
 
@@ -32,6 +43,10 @@ process split_target_RES_sequences {
 
     """
     get_targets_from_db.py -f ${fasta_file} -t ${targets_file} -o CHECK_
+
+    # Clean
+    unlink ${fasta_file}
+    unlink ${targets_file}
     """
 }
 
@@ -57,7 +72,10 @@ process split_target_RES_seq_from_sam_file {
 
     touch dummy_dummy_${pair_id}_dummy.bam
     touch dummy_dummy_${pair_id}_dummy.bai
-    find . \\! -type f \\( -name "*_*_${pair_id}*.bam" -o -name "*_*_${pair_id}*.bai" \\) -delete
+
+    # Clean directory
+    unlink ${bam_file}
+    unlink ${targets_file}
     """
 }
 
@@ -73,16 +91,31 @@ process freebayes {
     tuple val(pair_id), file("${pair_id}_consensus_seq.fna"), emit: consensus
 
     """
-
     for check_bam_file in CHECK_*_${pair_id}*.bam; do
         target=\$(echo \${check_bam_file} | sed 's/CHECK_//g' | sed 's/_${pair_id}.*//g')
         freebayes -q 20 -p 1 -f CHECK_\${target}_ref.fna \${check_bam_file} -v CHECK_\${target}_${pair_id}_seq.vcf
         bgzip CHECK_\${target}_${pair_id}_seq.vcf
         tabix -p vcf CHECK_\${target}_${pair_id}_seq.vcf.gz
         cat CHECK_\${target}_ref.fna | vcf-consensus CHECK_\${target}_${pair_id}_seq.vcf.gz >> ${pair_id}_consensus_seq.fna
+        rm CHECK_\${target}_${pair_id}_seq.vcf.gz
+        rm CHECK_\${target}_${pair_id}_seq.vcf.gz.tbi
+        rm CHECK_\${target}_ref.fna.fai
     done
 
     touch ${pair_id}_consensus_seq.fna
-    find . \\! -name "${pair_id}_consensus_seq.fna" -delete
+
+    # Clean directory
+    for check_bam_file in CHECK_*_${pair_id}*.bam; do
+        target=\$(echo \${check_bam_file} | sed 's/CHECK_//g' | sed 's/_${pair_id}.*//g')
+        unlink \${check_bam_file}
+        unlink CHECK_\${target}_${pair_id}_seq.bai
+        unlink CHECK_\${target}_ref.fna
+    done
+
+    mkdir output
+    mv ${pair_id}_consensus_seq.fna output
+    find . -maxdepth 1 -type f -delete
+    mv output/${pair_id}_consensus_seq.fna .
+    rm -d output
     """
 }
diff --git a/modules/serotyping.nf b/modules/serotyping.nf
index a2abac3..bad9e95 100644
--- a/modules/serotyping.nf
+++ b/modules/serotyping.nf
@@ -21,6 +21,14 @@ process serotyping {
     process_serotyper_results.py --srst2_output SERO_${pair_id} --sero_db ${sero_gene_db} --output ${pair_id}_SeroType_Results.txt --min_read_depth ${min_read_depth}
 
     touch ${output_file}
-    find . \\! -name ${output_file} -delete
+
+    # Clean directory
+    mkdir output
+    mv ${output_file} output
+    find . -maxdepth 1 -type f -delete
+    unlink ${reads[0]}
+    unlink ${reads[1]}
+    mv output/${output_file} .
+    rm -d output
     """
 }
diff --git a/modules/surface_typer.nf b/modules/surface_typer.nf
index 7230898..cb74ee6 100644
--- a/modules/surface_typer.nf
+++ b/modules/surface_typer.nf
@@ -20,6 +20,15 @@ process surface_typer {
 
     touch ${inc_output_file}
     touch ${variants_output_file}
-    find . \\! -type f \\( -name ${inc_output_file} -o -name ${variants_output_file} \\) -delete
+
+    # Clean directory
+    mkdir output
+    mv ${inc_output_file} output
+    mv ${variants_output_file} output
+    find . -maxdepth 1 -type f -delete
+    unlink ${surface_protein_db}
+    mv output/${inc_output_file} .
+    mv output/${variants_output_file} .
+    rm -d output
     """
 }