Regressive patch for compression (nf-core#5753)

* Regressive patch for compression

* Update tcs test and remove stdout file

* remoe test

modules/nf-core/tcoffee/align/main.nf

@@ -27,19 +27,26 @@ process TCOFFEE_ALIGN {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def tree_args = tree ? "-usetree $tree" : ""
     def template_args = template ? "-template_file $template" : ""
-    def write_output = compress ? " >(pigz -cp ${task.cpus} > ${prefix}.aln.gz)" : "> ${prefix}.aln"
-    // using >() is necessary to preserve the tcoffee return value,
-    // so nextflow knows to display an error when it failed
+    def outfile = compress ? "stdout" : "${prefix}.aln"
+    def write_output = compress ? " | pigz -cp ${task.cpus} > ${prefix}.aln.gz" : ""
     """
     export TEMP='./'
     t_coffee -seq ${fasta} \
         $tree_args \
         $template_args \
         $args \
         -thread ${task.cpus} \
-        -outfile stdout \
+        -outfile $outfile \
         $write_output
 
+    # If stdout file exist and compress is true, then compress the file
+    # This is a patch for the current behaviour of the regressive algorithm
+    # that does not support the stdout redirection
+    if [ -f stdout ] && [ "$compress" = true ]; then
+        pigz -cp ${task.cpus} < stdout > ${prefix}.aln.gz
+        rm stdout
+    fi
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         tcoffee: \$( t_coffee -version | awk '{gsub("Version_", ""); print \$3}')

modules/nf-core/tcoffee/tcs/tests/lib.config

@@ -1,5 +1,5 @@
 process {
     withName: "TCOFFEE_ALIGN"{
-        ext.args = { "-output fasta_aln -out_lib=sample_lib1.tc_lib" }
+        ext.args = { "-output fasta_aln -out_lib sample_lib1.tc_lib" }
     }
-}
+}