.

Author: DaanJansen94

nf-metatropics/assets/output/README.md

@@ -36,7 +36,7 @@ This stage optionally performs rarefaction, then removes low-quality reads, shor
 | `Reads/rarefaction` | Optional: Per-sample FASTQ after optional rarefaction subsampling. |
 | `Reads/nanoplot` | Read-length and quality summaries (NanoPlot) on the raw reads. |
 | `Reads/fastplong` | Trimmed, length-filtered reads (`*.fastp.fastq.gz`). |
-| `Reads/nohuman` | Human-depleted reads (`*_human_depleted.fastq.gz`); mapped reads (`*_human.fastq.gz`). |
+| `Reads/nohuman` | Human-depleted reads only (`*_human_depleted.fastq.gz`). Mapped human reads are not written, to avoid storing identifiable human genetic data (privacy / GDPR — genetic data is special-category personal data under [EU Regulation 2016/679](https://eur-lex.europa.eu/eli/reg/2016/679/oj)). |
 | `Reads/nohost` | Host-depleted reads (`*_host_depleted.fastq.gz`); mapped reads (`*_host.fastq.gz`). |
 
 ---

nf-metatropics/conf/modules.config

@@ -146,22 +146,15 @@ process {
             pattern: '*.fastq.gz',
             saveAs: { filename ->
                 def fn = filename.toString().tokenize('/').last()
-                // Rename / filter for human mapping:
-                //   *_other.fastq.gz     -> *_human_depleted.fastq.gz (reads NOT mapped to human; downstream input)
-                //   *_1.fastq.gz         -> *_human.fastq.gz          (reads mapped to human)
-                //   *_singleton.fastq.gz -> dropped
+                // Publish depleted reads only (never mapped human reads — privacy).
+                //   *_other.fastq.gz -> *_human_depleted.fastq.gz
                 if (fn.endsWith('_other.fastq.gz')) {
                     return fn.replaceFirst(/_other\.fastq\.gz$/, '_human_depleted.fastq.gz')
                 }
-                if (fn.endsWith('_1.fastq.gz')) {
-                    return fn.replaceFirst(/_1\.fastq\.gz$/, '_human.fastq.gz')
-                }
                 return null
             }
         ]
-        // Flags (-f/-F) are handled inside the module so it can emit BOTH:
-        //   mapped reads   -> *_1.fastq.gz
-        //   unmapped reads -> *_other.fastq.gz
+        // Flags (-f/-F) are handled inside the module (unmapped / depleted only).
         ext.args = ""
     }