add gzip checks in gather step

bactopia · Aug 26, 2023 · 2da04df · 2da04df
1 parent a64b215
commit 2da04df
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Showing 3 changed files with 210 additions and 46 deletions.
diff --git a/modules/local/bactopia/gather/main.nf b/modules/local/bactopia/gather/main.nf
@@ -189,16 +189,52 @@ process GATHER {
                 rm -f ${prefix}-paired-end-error.txt
             fi
 
-            if ! check-fastqs.py --fq1 r1.json --fq2 r2.json \${OPTS}; then
-                ERROR=1
+            if [[ -s r1.json ]] && [[ -s r2.json ]]; then
+                if ! check-fastqs.py --fq1 r1.json --fq2 r2.json \${OPTS}; then
+                    ERROR=1
+                fi
+            else
+                NOT_GZIP=0
+                if ! gzip -t fastqs/${prefix}_R1.fastq.gz; then
+                    NOT_GZIP=1
+                elif ! gzip -t fastqs/${prefix}_R2.fastq.gz; then
+                    NOT_GZIP=1
+                fi
+
+                if [ "\${NOT_GZIP}" -eq "0" ]; then
+                    echo "${prefix} FASTQs are empty. Please check the input FASTQs.
+                        Further analysis is discontinued." | \\
+                    sed 's/^\\s*//' > ${prefix}-empty-error.txt
+                    ERROR=1
+                else
+                    echo "${prefix} FASTQs failed Gzip tests. Please check the input FASTQs.
+                        Further analysis is discontinued." | \\
+                    sed 's/^\\s*//' > ${prefix}-gzip-error.txt
+                    ERROR=1
+                fi
             fi
             rm r1.json r2.json
         else
             # Single-end
             IS_PAIRED="false"
             gzip -cd fastqs/${prefix}.fastq.gz | fastq-scan > r1.json
-            if ! check-fastqs.py --fq1 r1.json \${OPTS}; then
-                ERROR=1
+
+            if [[ -s r1.json ]]; then
+                if ! check-fastqs.py --fq1 r1.json \${OPTS}; then
+                    ERROR=1
+                fi
+            else
+                if ! gzip -t fastqs/${prefix}.fastq.gz; then
+                    echo "${prefix} FASTQs failed Gzip tests. Please check the input FASTQs.
+                        Further analysis is discontinued." | \\
+                    sed 's/^\\s*//' > ${prefix}-gzip-error.txt
+                    ERROR=1
+                elif ! gzip -t fastqs/${prefix}_R2.fastq.gz; then
+                    echo "${prefix} FASTQs are empty. Please check the input FASTQs.
+                        Further analysis is discontinued." | \\
+                    sed 's/^\\s*//' > ${prefix}-empty-error.txt
+                    ERROR=1
+                fi
             fi
             rm r1.json
         fi

diff --git a/subworkflows/local/gather/test.nf b/subworkflows/local/gather/test.nf
@@ -163,3 +163,27 @@ workflow test_gather_error_low_depth_se {
 
     GATHER ( inputs )
 }
+
+workflow test_gather_empty_pe {
+
+    inputs = tuple(
+        [id:'output', runtype:'paired-end', genome_size:params.genome_size],
+        [file(params.test_data['empty']['fastq'], checkIfExists: true)],
+        [file(params.test_data['empty']['fastq'], checkIfExists: true)],
+        file(params.test_data['empty']['fna'], checkIfExists: true)
+    )
+
+    GATHER ( inputs )
+}
+
+workflow test_gather_empty_se {
+
+    inputs = tuple(
+        [id:'output', runtype:'single-end', genome_size:params.genome_size],
+        [file(params.test_data['empty']['fastq'], checkIfExists: true)],
+        [file(params.test_data['empty']['fastq'], checkIfExists: true)],
+        file(params.test_data['empty']['fna'], checkIfExists: true)
+    )
+
+    GATHER ( inputs )
+}