Merge pull request #17 from hoelzer/revision

Revision

main.nf

@@ -13,10 +13,53 @@ println "Starting time: $nextflow.timestamp"
 println "Workdir location:"
 println "  $workflow.workDir\u001B[0m"
 println " "
+// error codes
+if (params.profile) { exit 1, "--profile is WRONG use -profile" }
+if ( !workflow.revision ) { 
+  println "\033[0;33mWARNING: It is recommended to use a stable relese version via -r." 
+  println "Use 'nextflow info hoelzer/pocp' to check for available release versions.\033[0m\n"
+}
+// help
 if (params.help) { exit 0, helpMSG() }
+// input error codes
 if (params.genomes == '' && params.proteins == '') {exit 1, "input missing, use either [--genomes] or [--proteins]"}
 if (params.genomes != '' && params.proteins != '') {exit 1, "provide one input, use either [--genomes] or [--proteins]"}
 if (params.genome && params.protein) {exit 1, "provide only one input, use either [--genome] or [--protein]"}
+// print if default params are used:
+if (params.evalue == '1e-5' && params.seqidentity == 0.4 && params.alnlength == 0.5 && !params.blastp ) {
+  if ( !workflow.revision ) { 
+  println "\u001B[32mPOCP-nf was executed \033[0;31mwithout a stable release version\033[0m\u001B[32m and default paramters according to the original publication by Qin et al. (2014)."
+  } else {
+  println "\u001B[32mPOCP-nf was executed in version '${workflow.revision}' with default paramters according to the original publication by Qin et al. (2014)."
+  }
+  println ""
+  println "e-value:\t\t${params.evalue}"
+  println "Sequence identity:\t${params.seqidentity}"
+  println "Alignment length:\t${params.alnlength}"
+  println "\033[0m"
+  // print if NO default params are used
+} else {
+  if ( !workflow.revision ) { 
+  println "\033[0;31mPOCP-nf was executed without a stable release version and non-default paramters in comparison to the original publication by Qin et al. (2014)."
+  println ""
+  println "e-value used:\t\t${params.evalue}\t(original definition: 1e-5)"
+  println "Sequence identity used:\t${params.seqidentity}\t(original definition: 0.4)"
+  println "Alignment length used:\t${params.alnlength}\t(original definition: 0.5)"
+  } else {
+  println "\033[0;31mPOCP-nf was executed in version '${workflow.revision}' with non-default paramters in comparison to the original publication by Qin et al. (2014)."
+  println ""
+  println "e-value used:\t\t${params.evalue}\t(original definition: 1e-5)"
+  println "Sequence identity used:\t${params.seqidentity}\t(original definition: 0.4)"
+  println "Alignment length used:\t${params.alnlength}\t(original definition: 0.5)"
+  }
+  println ""
+  println "This will change your POCP results."
+  println "If you really want to use adjusted parameters, you must report them together with the used version of POCP-nf to ensure reproducibility!"
+  println ""
+  println "\033[0m"
+}
+
+
 
 // genomes fasta input & --list support
 if (params.genomes && params.list) { genome_input_ch = Channel
@@ -155,7 +198,7 @@ def helpMSG() {
     --evalue            Evalue for DIAMOND protein search [default: $params.evalue]
     --seqidentity       Sequence identity for DIAMOD alignments [default: $params.seqidentity]
     --alnlength         Alignment length for DIAMOND hits [default: $params.alnlength]
-    --blastp            Use BLASTP instead of DIAMOND for protein alignment (slower, as in the original 2014 publication) [default: $params.blastp]
+    --blastp            Use BLASTP instead of DIAMOND for protein alignment (slower but as in the original 2014 publication) [default: $params.blastp]
 
     ${c_dim}Nextflow options:
     -with-report rep.html    cpu / ram usage (may cause errors)