Test

data/templates/0.mapping_minimap2_db.sbatch

@@ -5,10 +5,11 @@
 #SBATCH -n {{nprocs}}
 #SBATCH --time {{wall_time_limit}}
 #SBATCH --mem {{mem_in_gb}}G
-#SBATCH -o {{output}}/step-1/logs/%x-%A_%a.out
-#SBATCH -e {{output}}/step-1/logs/%x-%A_%a.out
+#SBATCH -o {{output}}/step-0/logs/%x-%A_%a.out
+#SBATCH -e {{output}}/step-0/logs/%x-%A_%a.out
 #SBATCH --array {{array_params}}
 
+source ~/.bashrc
 conda activate {{conda_environment}}
 
 
@@ -21,4 +22,4 @@ filename=`echo $input | awk '{print $2}'`
 
 fn=`basename ${filename}`
 
-minimap2 -x map-hifi -t {{nprocs}} -a --secondary=no --MD --eqx -o {{output}}/step-0/${sample_name}.sam /projects/wol/qiyun/wol2/databases/minimap2/WoLr2.mmi ${filename}
+minimap2 -x map-hifi -t {{nprocs}} -a --secondary=no --MD --eqx  /projects/wol/qiyun/wol2/databases/minimap2/WoLr2.mmi ${filename} | samtools sort -@ {{nprocs}} -o {{output}}/step-1/${sample_name}_WoLr2.sorted.sam

data/templates/1.hifiasm-meta_new.sbatch

@@ -8,7 +8,7 @@
 #SBATCH -o {{output}}/step-1/logs/%x-%A_%a.out
 #SBATCH -e {{output}}/step-1/logs/%x-%A_%a.out
 #SBATCH --array {{array_params}}
-
+source ~/.bashrc
 conda activate {{conda_environment}}
 
 cd {{output}}/step-1

data/templates/2.get-circular-genomes.sbatch

@@ -9,6 +9,7 @@
 #SBATCH -e {{output}}/step-2/logs/%x-%A_%a.out
 #SBATCH --array {{array_params}}
 
+source ~/.bashrc
 
 conda activate {{conda_environment}}
 

data/templates/3.minimap2_assembly.sbatch

@@ -9,7 +9,7 @@
 #SBATCH -e {{output}}/step-3/logs/%x-%A_%a.err
 #SBATCH --array {{array_params}}
 
-
+source ~/.bashrc
 conda activate {{conda_environment}}
 cd {{output}}
 

data/templates/4.metawrap_binning_new.sbatch

@@ -9,6 +9,7 @@
 #SBATCH -e {{output}}/step-4/logs/%x-%A_%a.out
 #SBATCH --array {{array_params}}
 
+source ~/.bashrc
 conda activate {{conda_environment}}
 
 cd {{output}}
@@ -26,5 +27,5 @@ cp {{output}}/step-3/${sample_name}_binning/${sample_name}.sorted.bam {{output}}
 rm {{output}}/step-3/${sample_name}_binning/${sample_name}.sorted.bam
 
 ln -s ${filename} {{output}}/step-4/${sample_name}_binning/work_files/${sample_name}.fastq
-metawrap binning -a {{output}}/step-2/${sample_name}.noLCG.fa -o {{output}}/step-4/${sample_name}_binning \
+metawrap binning -a {{output}}/step-2/${sample_name}_noLCG.fa -o {{output}}/step-4/${sample_name}_binning \
    -t {{nprocs}} -m 100 -l 16000 --single-end --metabat2 --maxbin2 --concoct --universal {{output}}/step-4/${sample_name}_binning/work_files/${sample_name}.fastq

data/templates/5.DAS_Tools_prepare_batch3_test.sbatch

@@ -9,6 +9,8 @@
 #SBATCH -e {{output}}/step-5/logs/%x-%A_%a.out
 #SBATCH --array {{array_params}}
 
+source ~/.bashrc
+
 conda activate {{conda_environment}}
 cd {{output}}
 
@@ -33,4 +35,4 @@ Fasta_to_Contig2Bin.sh -i ./concoct_bins -e fa > ${sample_name}.concoct.tsv
 Fasta_to_Contig2Bin.sh -i ./maxbin2_bins -e fa > ${sample_name}.maxbin2.tsv
 Fasta_to_Contig2Bin.sh -i ./metabat2_bins -e fa > ${sample_name}.metabat2.tsv
 
-DAS_Tool --bins=${sample_name}.concoct.tsv,${sample_name}.maxbin2.tsv,${sample_name}.metabat2.tsv --contigs={{output}}/step-2/${sample_name}.noLCG.fa --outputbasename={{output}}/${folder}/${sample_name}/${sample_name} --labels=CONCOCT,MaxBin,MetaBAT --threads={{nprocs}} --search_engine=diamond --dbDirectory=${DAS_db} --write_bins
+DAS_Tool --bins=${sample_name}.concoct.tsv,${sample_name}.maxbin2.tsv,${sample_name}.metabat2.tsv --contigs={{output}}/step-2/${sample_name}_noLCG.fa --outputbasename={{output}}/${folder}/${sample_name}/${sample_name} --labels=CONCOCT,MaxBin,MetaBAT --threads={{nprocs}} --search_engine=diamond --dbDirectory=${DAS_db} --write_bins

data/templates/6.MAG_rename.sbatch

@@ -9,6 +9,7 @@
 #SBATCH -e {{output}}/step-6/logs/%x-%A_%a.out
 #SBATCH --array {{array_params}}
 
+source ~/.bashrc
 conda activate {{conda_environment}}
 cd {{output}}
 

data/templates/7.checkm_batch.sbatch

@@ -9,6 +9,9 @@
 #SBATCH -e {{output}}/step-7/logs/%x-%A_%a.out
 #SBATCH --array {{array_params}}
 
+
+source ~/.bashrc
+
 conda activate {{conda_environment}}
 
 cd {{output}}

qp_pacbio/tests/test_pacbio.py

@@ -6,37 +6,54 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-from unittest import main
-from qiita_client import ArtifactInfo
-from qiita_client.testing import PluginTestCase
+from json import dumps
 from os import remove
 from os.path import exists, isdir, join
+from shutil import copyfile, rmtree
 from tempfile import mkdtemp
-from shutil import rmtree, copyfile
-from json import dumps
+from unittest import main
+
+from qiita_client import ArtifactInfo
+from qiita_client.testing import PluginTestCase
 
 from qp_pacbio import plugin
 from qp_pacbio.qp_pacbio import pacbio_processing
 
+# Keep these in sync with your generator defaults
+CONDA_ENV = "qp_pacbio_2025.9"
+STEP1_NPROCS = 16
+STEP1_WALL = 1000
+STEP1_MEM_GB = 300  # generator uses 300G for step-1
+NODE_COUNT = 1
+PARTITION = "qiita"
 
+# Exact expected Step-1 script matching your template.
+# Escape ${...} -> ${{...}} and awk braces -> '{{print $1}}' etc.
 STEP_1_EXP = (
     "#!/bin/bash\n"
-    "#SBATCH -J s1-my-job-id\n"
-    "#SBATCH -N 1\n"
-    "#SBATCH -n 32\n"
-    "#SBATCH --time 1000\n"
-    "#SBATCH --mem 300G\n"
-    "#SBATCH -o {out_dir}/step-1/logs/%x-%A.out\n"
-    "#SBATCH -e {out_dir}/step-1/logs/%x-%A.err\n"
-    "#SBATCH --array 1:2%16\n"
-    "\n"
-    "conda activate qp_pacbio_2025.9\n"
+    "#SBATCH -J s1-{job_id}\n"
+    f"#SBATCH -p {PARTITION}\n"
+    f"#SBATCH -N {NODE_COUNT}\n"
+    f"#SBATCH -n {STEP1_NPROCS}\n"
+    f"#SBATCH --time {STEP1_WALL}\n"
+    f"#SBATCH --mem {STEP1_MEM_GB}G\n"
+    "#SBATCH -o {out_dir}/step-1/logs/%x-%A_%a.out\n"
+    "#SBATCH -e {out_dir}/step-1/logs/%x-%A_%a.out\n"
+    "#SBATCH --array 1-{njobs}%16\n"
+    "source ~/.bashrc\n"
+    f"conda activate {CONDA_ENV}\n"
     "\n"
     "cd {out_dir}/step-1\n"
     "step=${{SLURM_ARRAY_TASK_ID}}\n"
-    "input=$(head -n $step {out_dir}/file_list.txt | tail -n 1)\n"
-    "fn=`basename ${{input}}`\n"
-    "hifiasm_meta -t 60 -o {out_dir}/step-1/${{fn}} ${{input}}"
+    "input=$(head -n $step {out_dir}/sample_list.txt | tail -n 1)\n"
+    "\n"
+    "sample_name=`echo $input | awk '{{print $1}}'`\n"
+    "filename=`echo $input | awk '{{print $2}}'`\n"
+    "\n"
+    "fn=`basename ${{filename}}`\n"
+    "\n"
+    f"hifiasm_meta -t {STEP1_NPROCS} -o "
+    "{out_dir}/step-1/${{sample_name}} ${{filename}}"
 )
 
 
@@ -110,14 +127,18 @@ def test_pacbio_processing(self):
         with open(f"{out_dir}/sample_list.txt", "r") as f:
             obs_lines = f.readlines()
         self.assertEqual(2, len(obs_lines))
-
+        njobs = len(obs_lines)
         # testing step-1
         with open(f"{out_dir}/step-1/step-1.slurm", "r") as f:
             # removing \n
             obs_lines = [ln.replace("\n", "") for ln in f.readlines()]
 
         self.assertCountEqual(
-            STEP_1_EXP.format(out_dir=out_dir).split("\n"),
+            STEP_1_EXP.format(
+                out_dir=out_dir,
+                job_id=job_id,
+                njobs=njobs,
+            ).split("\n"),
             obs_lines,
         )