更新 .gitignore，添加 run.status.json；删除旧的 mapping.sh 脚本并添加新的 01.mapping.sh 脚本

.gitignore

@@ -10,9 +10,10 @@
 05.reduce_redundancy/*
 05.orthology_inference/*
 06.phylogeny_reconstruction/*
+10.plastid/*
 98.results/*
 99.scripts/bucky/
 99.scripts/phyparts/
-run.status
+run.status.json
 !*/_description.md
 tmp/

99.scripts/workflow/plastid/01.mapping.sh

@@ -0,0 +1,18 @@
+#! /bin/bash
+set -e
+THREADS=${THREADS:-6}
+if [ "$#" -ne 4 ]; then
+    echo "Usage: $0 <reference_genome> <fastq_1> <fastq_2> <output_prefix>"
+    exit 1
+fi
+
+ref=$1
+fq1=$2
+fq2=$3
+out=$4
+outdir=$(dirname "$out")
+mkdir -p "$outdir"
+hisat2 -p "$THREADS" --dta -x "$ref" -1 "$fq1" -2 "$fq2" -S "${out}.sam"
+samtools view -b -@ "$THREADS" "${out}.sam" | samtools sort -@ "$THREADS" -o "${out}.sorted.bam" --write-index
+rm "${out}.sam"
+echo "Mapping completed. Sorted BAM file is at ${out}.sorted.bam"

99.scripts/workflow/plastid/mapping.sh

@@ -1,15 +0,0 @@
-#! /usr/bash
-if [ "$#" -ne 5 ]; then
-    echo "Usage: $0 <reference_genome> <fastq_1> <fastq_2> <output_directory> <stem>"
-    exit 1
-fi
-ref=$1
-fq1=$2
-fq2=$3
-outdir=$4
-stem=$5
-mkdir -p "$outdir"
-hisat -p 4 --dta -x "$ref" -1 "$fq1" -2 "$fq2" -S "${outdir}/${stem}.sam"
-samtools view -b -@ 4 "${outdir}/${stem}.sam" | samtools sort -@ 4 -o "${outdir}/${stem}.sorted.bam" --write-index
-rm "${outdir}/${stem}.sam"
-echo "Mapping completed. Sorted BAM file is at ${outdir}/${stem}.sorted.bam"