diff --git a/data/templates/0.mapping_minimap2_db.sbatch b/data/templates/0.mapping_minimap2_db.sbatch
deleted file mode 100644
index c158c3a..0000000
--- a/data/templates/0.mapping_minimap2_db.sbatch
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/bash
-#SBATCH -J {{job_name}}
-#SBATCH -p qiita
-#SBATCH -N {{node_count}}
-#SBATCH -n {{nprocs}}
-#SBATCH --time {{wall_time_limit}}
-#SBATCH --mem {{mem_in_gb}}G
-#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}}
-
-
-cd {{output}}/step-0
-step=${SLURM_ARRAY_TASK_ID} ##1000_2, 1000_1
-input=$(head -n $step {{output}}/sample_list.txt | tail -n 1)
-
-sample_name=`echo $input | awk '{print $1}'`
-filename=`echo $input | awk '{print $2}'`
-
-fn=`basename ${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
\ No newline at end of file
diff --git a/data/templates/1.hifiasm-meta_new.sbatch b/data/templates/1.hifiasm-meta_new.sbatch
index febbea2..5b6c8c4 100644
--- a/data/templates/1.hifiasm-meta_new.sbatch
+++ b/data/templates/1.hifiasm-meta_new.sbatch
@@ -8,10 +8,12 @@
 #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
+set -e
 conda activate {{conda_environment}}
-
 cd {{output}}/step-1
+
 step=${SLURM_ARRAY_TASK_ID}
 input=$(head -n $step {{output}}/sample_list.txt | tail -n 1)
 
diff --git a/data/templates/2.get-circular-genomes.sbatch b/data/templates/2.get-circular-genomes.sbatch
index 65a7ba6..dadd114 100644
--- a/data/templates/2.get-circular-genomes.sbatch
+++ b/data/templates/2.get-circular-genomes.sbatch
@@ -10,9 +10,8 @@
 #SBATCH --array {{array_params}}
 
 source ~/.bashrc
-
+set -e
 conda activate {{conda_environment}}
-
 cd {{output}}/step-1
 
 step=${SLURM_ARRAY_TASK_ID} ##1000_2, 1000_1
diff --git a/data/templates/3.minimap2_assembly.sbatch b/data/templates/3.minimap2_assembly.sbatch
index f854ba3..36c14b6 100644
--- a/data/templates/3.minimap2_assembly.sbatch
+++ b/data/templates/3.minimap2_assembly.sbatch
@@ -10,6 +10,7 @@
 #SBATCH --array {{array_params}}
 
 source ~/.bashrc
+set -e
 conda activate {{conda_environment}}
 cd {{output}}
 
diff --git a/data/templates/4.metawrap_binning_new.sbatch b/data/templates/4.metawrap_binning_new.sbatch
index 66cd380..310f415 100644
--- a/data/templates/4.metawrap_binning_new.sbatch
+++ b/data/templates/4.metawrap_binning_new.sbatch
@@ -10,8 +10,8 @@
 #SBATCH --array {{array_params}}
 
 source ~/.bashrc
+set -e
 conda activate {{conda_environment}}
-
 cd {{output}}
 
 step=${SLURM_ARRAY_TASK_ID}
diff --git a/data/templates/5.DAS_Tools_prepare_batch3_test.sbatch b/data/templates/5.DAS_Tools_prepare_batch3_test.sbatch
index f328ec2..2c175be 100755
--- a/data/templates/5.DAS_Tools_prepare_batch3_test.sbatch
+++ b/data/templates/5.DAS_Tools_prepare_batch3_test.sbatch
@@ -10,7 +10,7 @@
 #SBATCH --array {{array_params}}
 
 source ~/.bashrc
-
+set -e
 conda activate {{conda_environment}}
 cd {{output}}
 
@@ -35,4 +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
\ No newline at end of file
+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
diff --git a/data/templates/6.MAG_rename.sbatch b/data/templates/6.MAG_rename.sbatch
index 6cf89a1..8748a04 100644
--- a/data/templates/6.MAG_rename.sbatch
+++ b/data/templates/6.MAG_rename.sbatch
@@ -10,6 +10,7 @@
 #SBATCH --array {{array_params}}
 
 source ~/.bashrc
+set -e
 conda activate {{conda_environment}}
 cd {{output}}
 
diff --git a/data/templates/7.checkm_batch.sbatch b/data/templates/7.checkm_batch.sbatch
index 8c0fb0f..d90dd29 100644
--- a/data/templates/7.checkm_batch.sbatch
+++ b/data/templates/7.checkm_batch.sbatch
@@ -11,9 +11,8 @@
 
 
 source ~/.bashrc
-
+set -e
 conda activate {{conda_environment}}
-
 cd {{output}}
 
 step=${SLURM_ARRAY_TASK_ID}
diff --git a/data/templates/woltka_minimap2.sbatch b/data/templates/woltka_minimap2.sbatch
new file mode 100644
index 0000000..7f01603
--- /dev/null
+++ b/data/templates/woltka_minimap2.sbatch
@@ -0,0 +1,32 @@
+#!/bin/bash
+#SBATCH -J {{job_name}}
+#SBATCH -p qiita
+#SBATCH -N {{node_count}}
+#SBATCH -n {{nprocs}}
+#SBATCH --time {{wall_time_limit}}
+#SBATCH --mem {{mem_in_gb}}G
+#SBATCH -o {{output}}/minimap2/logs/%x-%A_%a.out
+#SBATCH -e {{output}}/minimap2/logs/%x-%A_%a.out
+#SBATCH --array {{array_params}}
+
+source ~/.bashrc
+set -e
+conda activate {{conda_environment}}
+mkdir -p {{output}}/alignments
+cd {{output}}/
+db=/ddn_scratch/qiita_t/working_dir/tmp/db/WoLr2.mmi
+
+step=${SLURM_ARRAY_TASK_ID}
+input=$(head -n $step {{output}}/sample_list.txt | tail -n 1)
+
+sample_name=`echo $input | awk '{print $1}'`
+filename=`echo $input | awk '{print $2}'`
+
+fn=`basename ${filename}`
+
+minimap2 -x map-hifi -t {{nprocs}} -a \
+       --secondary=no --MD --eqx ${db} \
+       ${filename} | \
+   samtools sort -@ {{nprocs}} - | \
+   awk 'BEGIN { FS=OFS="\t" } /^@/ { print; next } { $10="*"; $11="*" } 1' | \
+   xz -1 -T1 > {{output}}/alignments/${sample_name}.sam.xz
diff --git a/data/templates/woltka_minimap2_merge.sbatch b/data/templates/woltka_minimap2_merge.sbatch
new file mode 100644
index 0000000..dc35979
--- /dev/null
+++ b/data/templates/woltka_minimap2_merge.sbatch
@@ -0,0 +1,49 @@
+#!/bin/bash
+#SBATCH -J {{job_name}}
+#SBATCH -p qiita
+#SBATCH -N {{node_count}}
+#SBATCH -n {{nprocs}}
+#SBATCH --time {{wall_time_limit}}
+#SBATCH --mem {{mem_in_gb}}G
+#SBATCH -o {{output}}/merge/logs/%x-%A_%a.out
+#SBATCH -e {{output}}/merge/logs/%x-%A_%a.out
+
+source ~/.bashrc
+set -e
+conda activate {{conda_environment}}
+cd {{output}}/
+tax=/projects/wol/qiyun/wol2/databases/minimap2/WoLr2.tax
+coords=/projects/wol/qiyun/wol2/databases/minimap2/WoLr2.coords
+len_map=/projects/wol/qiyun/wol2/databases/minimap2/WoLr2/length.map
+functional_dir=/projects/wol/qiyun/wol2/databases/minimap2/WoLr2/
+
+mkdir -p {{output}}/coverages/
+
+for f in `ls alignments/*.sam.xz`; do
+    sn=`basename ${f/.sam.xz/}`;
+    of={{output}}/bioms/${sn};
+    mkdir -p ${of};
+    echo "woltka classify -i ${f} -o ${of}/none.biom --no-demux --lineage ${tax} --rank none --outcov {{output}}/coverages/";
+    echo "woltka classify -i ${f} -o ${of}/per-gene.biom --no-demux -c ${coords}";
+done | parallel -j {{node_count}}
+wait
+
+for f in `ls bioms/*/per-gene.biom`; do
+    dn=`dirname ${f}`;
+    sn=`basename ${sn}`;
+    echo "woltka collapse -i ${f} -m ${functional_dir}/orf-to-ko.map.xz -o ${dn}/ko.biom; " \
+        "woltka collapse -i ${dn}/ko.biom -m ${functional_dir}/ko-to-ec.map -o ${dn}/ec.biom; " \
+        "woltka collapse -i ${dn}/ko.biom -m ${functional_dir}/ko-to-reaction.map -o ${dn}/reaction.biom; " \
+        "woltka collapse -i ${dn}/reaction.biom -m ${functional_dir}/reaction-to-module.map -o ${dn}/module.biom; " \
+        "woltka collapse -i ${dn}/module.biom -m ${functional_dir}/module-to-pathway.map -o ${dn}/pathway.biom;"
+done | parallel -j {{node_count}}
+wait
+
+# MISSING:
+# merge bioms!
+
+find {{output}}/coverages/ -iname "*.cov" > {{output}}/cov_files.txt
+micov consolidate --paths {{output}}/cov_files.txt --lengths ${len_map} --output {{output}}/coverages.tgz
+
+cd alignments
+tar -cvf ../alignments.tar *.sam.xz
diff --git a/qp_pacbio/__init__.py b/qp_pacbio/__init__.py
index c809957..e8221ff 100644
--- a/qp_pacbio/__init__.py
+++ b/qp_pacbio/__init__.py
@@ -6,11 +6,43 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 from qiita_client import QiitaPlugin, QiitaCommand
-from .qp_pacbio import pacbio_processing
+from .qp_pacbio import pacbio_processing, minimap2_processing
+from .util import plugin_details
 
-__version__ = "2025.9"
 
-plugin = QiitaPlugin("qp-pacbio", __version__, "PacBio Processing")
+plugin = QiitaPlugin(**plugin_details)
+
+#
+# minimap2 command
+#
+
+req_params = {'artifact_id': ('integer', ['per_sample_FASTQ'])}
+opt_params = dict()
+outputs = {
+    # taxonomic
+    'Per genome Predictions': 'BIOM',
+    'Per gene Predictions': 'BIOM',
+    # functional
+    'KEGG Ontology (KO)': 'BIOM',
+    'KEGG Enzyme (EC)': 'BIOM',
+    'KEGG Pathway': 'BIOM',
+    }
+dflt_param_set = dict()
+
+minimap2_cmd = QiitaCommand(
+    "Woltka v0.1.7, minimap2",
+    "Functional and Taxonomic Predictions",
+    minimap2_processing,
+    req_params,
+    opt_params,
+    outputs,
+    dflt_param_set,
+)
+plugin.register_command(minimap2_cmd)
+
+#
+# pacbio processing pipeline command
+#
 
 req_params = {
     "artifact_id": ("integer", [None]),
diff --git a/qp_pacbio/qp_pacbio.py b/qp_pacbio/qp_pacbio.py
index 143b756..ddb0637 100644
--- a/qp_pacbio/qp_pacbio.py
+++ b/qp_pacbio/qp_pacbio.py
@@ -5,12 +5,16 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
-from os import makedirs
+from os import makedirs, mkdir
 from os.path import basename, join, exists, getmtime
 import pathlib
+from shutil import copy2
+
 
 from jinja2 import Environment, BaseLoader, TemplateNotFound
 from qiita_client import ArtifactInfo
+from subprocess import run
+
 
 CONDA_ENV = "qp_pacbio_2025.9"
 MAX_WALL_1000 = 1000
@@ -18,6 +22,11 @@
 T5_NAME = "5.DAS_Tools_prepare_batch3_test.sbatch"
 
 
+def sbatch(args):
+    res = run(args, check=True, capture_output=True, text=True)
+    return res.stdout.strip()
+
+
 # taken from qp-woltka
 def search_by_filename(fname, lookup):
     if fname in lookup:
@@ -67,8 +76,10 @@ def _write_slurm(path, template, **ctx):
     with open(out_fp, mode="w", encoding="utf-8") as f:
         f.write(rendered)
 
+    return out_fp
+
 
-def generate_templates(out_dir, job_id, njobs):
+def pacbio_generate_templates(out_dir, job_id, njobs):
     """Generate Slurm submission templates for PacBio processing.
 
     Parameters
@@ -82,21 +93,6 @@ def generate_templates(out_dir, job_id, njobs):
     """
     jinja_env = Environment(loader=KISSLoader("../data/templates"))
 
-    # Step 0
-    template0 = jinja_env.get_template("0.mapping_minimap2_db.sbatch")
-    _write_slurm(
-        join(out_dir, "step-0"),
-        template0,
-        conda_environment=CONDA_ENV,
-        output=out_dir,
-        job_name=f"s0-{job_id}",
-        node_count=1,
-        nprocs=16,
-        wall_time_limit=MAX_WALL_1000,
-        mem_in_gb=300,
-        array_params=f"1-{njobs}%16",
-    )
-
     # Step 1
     template1 = jinja_env.get_template("1.hifiasm-meta_new.sbatch")
     _write_slurm(
@@ -270,7 +266,7 @@ def pacbio_processing(qclient, job_id, parameters, out_dir):
         job_id,
         "Step 2 of 3: Creating submission templates",
     )
-    generate_templates(out_dir, job_id, njobs)
+    pacbio_generate_templates(out_dir, job_id, njobs)
 
     # If/when you enable submission, capture Slurm job IDs and thread them:
     # jid0 = qclient.submit_job(f"{out_dir}/step-0/step-0.slurm")
@@ -316,3 +312,130 @@ def pacbio_processing(qclient, job_id, parameters, out_dir):
         [ArtifactInfo("output", "job-output-folder", paths)],
         f"{job_id} completed.",
     )
+
+
+def minimap2_processing(qclient, job_id, parameters, out_dir):
+    """generates output for minimap2/woltka processing.
+
+    Parameters
+    ----------
+    qclient : tgp.qiita_client.QiitaClient
+        Qiita server client.
+    job_id : str
+        Job id.
+    parameters : dict
+        Parameters for this job.
+    out_dir : str
+        Output directory.
+
+    Returns
+    -------
+    bool, list, str
+        Results tuple for Qiita.
+    """
+    qclient.update_job_step(job_id, "Commands finished")
+
+    def _coverage_copy(dest):
+        fp_coverages = join(out_dir, 'coverages.tgz')
+        mkdir(dest)
+        dest = join(dest, 'coverages.tgz')
+        copy2(fp_coverages, dest)
+
+        return dest
+
+    errors = []
+    ainfo = []
+
+    fp_biom = f'{out_dir}/none.biom'
+    fp_alng = f'{out_dir}/alignment.tar'
+    if exists(fp_biom) and exists(fp_alng):
+        ainfo.append(ArtifactInfo('Per genome Predictions', 'BIOM', [
+            (fp_biom, 'biom'), (fp_alng, 'log'),
+            (_coverage_copy(f'{out_dir}/none/'), 'plain_text')]))
+    else:
+        errors.append('Table none/per-genome was not created, please contact '
+                      'qiita.help@gmail.com for more information')
+
+    bioms = [
+        (f'{out_dir}/per-gene.biom', 'per_gene' 'Per gene Predictions'),
+        (f'{out_dir}/ko.biom', 'ko' 'KEGG Ontology (KO)'),
+        (f'{out_dir}/ec.biom', 'ec' 'KEGG Enzyme (EC)'),
+        (f'{out_dir}/pathway.biom', 'pathway' 'KEGG Pathway'),
+    ]
+
+    for fb, fn, bn in bioms:
+        if exists(fb):
+            ainfo.append(ArtifactInfo(bn, 'BIOM', [
+                (fb, 'biom'),
+                (_coverage_copy(f'{out_dir}/{fn}/'), 'plain_text')]))
+        else:
+            errors.append(f'Table "{bn}" was not created, please contact '
+                          'qiita.help@gmail.com for more information')
+
+    if errors:
+        return False, ainfo, '\n'.join(errors)
+    else:
+
+        return True, ainfo, ""
+
+
+def generate_minimap2_processing(qclient, job_id, out_dir, parameters):
+    """generates slurm scripts for minimap2/woltka processing.
+
+    Parameters
+    ----------
+    qclient : tgp.qiita_client.QiitaClient
+        Qiita server client.
+    job_id : str
+        Job id.
+    out_dir : str
+        Output directory.
+    parameters : dict
+        Parameters for this job.
+
+    Returns
+    -------
+    str, str
+        Returns the two filepaths of the slurm scripts
+    """
+    qclient.update_job_step(
+        job_id, "Step 1 of 4: Collecting info and generating submission")
+
+    artifact_id = parameters["artifact_id"]
+
+    njobs = generate_sample_list(qclient, artifact_id, out_dir)
+
+    qclient.update_job_step(
+        job_id,
+        "Step 2 of 4: Creating submission templates",
+    )
+
+    jinja_env = Environment(loader=KISSLoader("../data/templates"))
+    minimap2_template = jinja_env.get_template("woltka_minimap2.sbatch")
+    minimap2_script = _write_slurm(
+        f'{out_dir}/minimap2',
+        minimap2_template,
+        conda_environment=CONDA_ENV,
+        output=out_dir,
+        job_name=f"m2_{job_id}",
+        node_count=1,
+        nprocs=16,
+        wall_time_limit=MAX_WALL_1000,
+        mem_in_gb=120,
+        array_params=f"1-{njobs}%16",
+    )
+    minimap2_merge_template = jinja_env.get_template(
+        "woltka_minimap2_merge.sbatch")
+    minimap2_merge_script = _write_slurm(
+        f'{out_dir}/merge',
+        minimap2_merge_template,
+        conda_environment=CONDA_ENV,
+        output=out_dir,
+        job_name=f"me_{job_id}",
+        node_count=1,
+        nprocs=16,
+        wall_time_limit=MAX_WALL_1000,
+        mem_in_gb=120
+    )
+
+    return minimap2_script, minimap2_merge_script
diff --git a/qp_pacbio/scripts.py b/qp_pacbio/scripts.py
index 69bc07e..0e0338f 100644
--- a/qp_pacbio/scripts.py
+++ b/qp_pacbio/scripts.py
@@ -8,6 +8,9 @@
 # -----------------------------------------------------------------------------
 import click
 from qp_pacbio import plugin
+from qp_pacbio.qp_pacbio import generate_minimap2_processing
+from qp_pacbio.util import client_connect
+from subprocess import run, PIPE
 
 
 @click.command()
@@ -32,4 +35,23 @@ def config(env_script, ca_cert):
 @click.argument("output_dir", required=True)
 def execute(url, job_id, output_dir):
     """Executes the task given by job_id and puts the output in output_dir"""
-    plugin(url, job_id, output_dir)
+    if 'register' in job_id:
+        plugin(url, job_id, output_dir)
+    else:
+        qclient = client_connect(url)
+        job_info = qclient.get_job_info(job_id)
+        parameters = job_info['parameters']
+
+        main_fp, merge_fp = generate_minimap2_processing(
+                qclient, job_id, output_dir, parameters)
+
+        # Submitting jobs and returning id
+        main_job = run(['sbatch', main_fp], stdout=PIPE)
+        main_job_id = main_job.stdout.decode('utf8').split()[-1]
+        merge_job = run(['sbatch', '-d', f'afterok:{main_job_id}',
+                         merge_fp], stdout=PIPE)
+        merge_job_id = merge_job.stdout.decode('utf8').split()[-1]
+        print(f'{main_job_id}, {merge_job_id}')
+
+        qclient.update_job_step(
+            job_id, "Step 2 of 4: Aligning sequences")
diff --git a/qp_pacbio/tests/test_pacbio.py b/qp_pacbio/tests/test_pacbio.py
index 30af8f7..c4d87a1 100644
--- a/qp_pacbio/tests/test_pacbio.py
+++ b/qp_pacbio/tests/test_pacbio.py
@@ -17,7 +17,7 @@
 from qiita_client.testing import PluginTestCase
 
 from qp_pacbio import plugin
-from qp_pacbio.qp_pacbio import pacbio_processing
+from qp_pacbio.qp_pacbio import generate_minimap2_processing, pacbio_processing
 
 # Keep these in sync with your generator defaults
 CONDA_ENV = "qp_pacbio_2025.9"
@@ -40,10 +40,12 @@
     "#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"
+    "\n"
     "source ~/.bashrc\n"
+    "set -e\n"
     f"conda activate {CONDA_ENV}\n"
-    "\n"
     "cd {out_dir}/step-1\n"
+    "\n"
     "step=${{SLURM_ARRAY_TASK_ID}}\n"
     "input=$(head -n $step {out_dir}/sample_list.txt | tail -n 1)\n"
     "\n"
@@ -112,6 +114,8 @@ def _insert_data(self):
 
         return aid
 
+
+class PacProcessingTests(PacBioTests):
     def test_pacbio_processing(self):
         params = {"artifact_id": self._insert_data()}
         job_id = "my-job-id"
@@ -153,5 +157,122 @@ def test_pacbio_processing(self):
         self.assertCountEqual(ainfo, exp)
 
 
+class PacWoltkaProfilingTests(PacBioTests):
+    def test_pacbio_processing(self):
+        params = {"artifact_id": int(self._insert_data())}
+        job_id = "my-job-id"
+        out_dir = mkdtemp()
+        self._clean_up_files.append(out_dir)
+
+        # this should fail cause we don't have valid data
+        main_fp, merge_fp = generate_minimap2_processing(
+                self.qclient, job_id, out_dir, params)
+        with open(main_fp, 'r') as f:
+            obs_main = f.readlines()
+        with open(merge_fp, 'r') as f:
+            obs_merge = f.readlines()
+
+        exp_main = [
+            '#!/bin/bash\n',
+            '#SBATCH -J m2_my-job-id\n',
+            '#SBATCH -p qiita\n',
+            '#SBATCH -N 1\n',
+            '#SBATCH -n 16\n',
+            '#SBATCH --time 1000\n',
+            '#SBATCH --mem 120G\n',
+            f'#SBATCH -o {out_dir}/minimap2/logs/%x-%A_%a.out\n',
+            f'#SBATCH -e {out_dir}/minimap2/logs/%x-%A_%a.out\n',
+            '#SBATCH --array 1-2%16\n',
+            '\n',
+            'source ~/.bashrc\n',
+            'set -e\n',
+            'conda activate qp_pacbio_2025.9\n',
+            f'mkdir -p {out_dir}/alignments\n',
+            f'cd {out_dir}/\n',
+            'db=/ddn_scratch/qiita_t/working_dir/tmp/db/WoLr2.mmi\n',
+            '\n',
+            'step=${SLURM_ARRAY_TASK_ID}\n',
+            f'input=$(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',
+            'minimap2 -x map-hifi -t 16 -a \\\n',
+            '       --secondary=no --MD --eqx ${db} \\\n',
+            '       ${filename} | \\\n',
+            '   samtools sort -@ 16 - | \\\n',
+            '   awk \'BEGIN { FS=OFS="\\t" } /^@/ { print; next } '
+            '{ $10="*"; $11="*" } 1\' | \\\n',
+            f'   xz -1 -T1 > {out_dir}/alignments/${{sample_name}}.sam.xz']
+        self.assertEqual(obs_main, exp_main)
+
+        db_path = '/projects/wol/qiyun/wol2/databases/minimap2'
+        exp_merge = [
+            '#!/bin/bash\n',
+            '#SBATCH -J me_my-job-id\n',
+            '#SBATCH -p qiita\n',
+            '#SBATCH -N 1\n',
+            '#SBATCH -n 16\n',
+            '#SBATCH --time 1000\n',
+            '#SBATCH --mem 120G\n',
+            f'#SBATCH -o {out_dir}/merge/logs/%x-%A_%a.out\n',
+            f'#SBATCH -e {out_dir}/merge/logs/%x-%A_%a.out\n',
+            '\n',
+            'source ~/.bashrc\n',
+            'set -e\n',
+            'conda activate qp_pacbio_2025.9\n',
+            f'cd {out_dir}/\n',
+            f'tax={db_path}/WoLr2.tax\n',
+            f'coords={db_path}/WoLr2.coords\n',
+            f'len_map={db_path}/WoLr2/length.map\n',
+            f'functional_dir={db_path}/WoLr2/\n',
+            '\n',
+            f'mkdir -p {out_dir}/coverages/\n',
+            '\n',
+            'for f in `ls alignments/*.sam.xz`; do\n',
+            '    sn=`basename ${f/.sam.xz/}`;\n',
+            f'    of={out_dir}/bioms/${{sn}};\n',
+            '    mkdir -p ${of};\n',
+            '    echo "woltka classify -i ${f} -o ${of}/none.biom '
+            '--no-demux --lineage ${tax} '
+            f'--rank none --outcov {out_dir}/coverages/";\n',
+            '    echo "woltka classify -i ${f} -o ${of}/per-gene.biom '
+            '--no-demux -c ${coords}";\n',
+            'done | parallel -j 1\n',
+            'wait\n',
+            '\n',
+            'for f in `ls bioms/*/per-gene.biom`; do\n',
+            '    dn=`dirname ${f}`;\n',
+            '    sn=`basename ${sn}`;\n',
+            '    echo "woltka collapse -i ${f} -m ${functional_dir}/'
+            'orf-to-ko.map.xz -o ${dn}/ko.biom; " \\\n',
+            '        "woltka collapse -i ${dn}/ko.biom -m ${functional_dir}/'
+            'ko-to-ec.map -o ${dn}/ec.biom; " \\\n',
+            '        "woltka collapse -i ${dn}/ko.biom -m ${functional_dir}/'
+            'ko-to-reaction.map -o ${dn}/reaction.biom; " \\\n',
+            '        "woltka collapse -i ${dn}/reaction.biom -m '
+            '${functional_dir}/reaction-to-module.map -o '
+            '${dn}/module.biom; " \\\n',
+            '        "woltka collapse -i ${dn}/module.biom -m '
+            '${functional_dir}/module-to-pathway.map '
+            '-o ${dn}/pathway.biom;"\n',
+            'done | parallel -j 1\n',
+            'wait\n',
+            '\n',
+            '# MISSING:\n',
+            '# merge bioms!\n',
+            '\n',
+            f'find {out_dir}/coverages/ -iname "*.cov" > '
+            f'{out_dir}/cov_files.txt\n',
+            f'micov consolidate --paths {out_dir}/cov_files.txt '
+            f'--lengths ${{len_map}} --output {out_dir}/coverages.tgz\n',
+            '\n',
+            'cd alignments\n',
+            'tar -cvf ../alignments.tar *.sam.xz']
+        self.assertEqual(obs_merge, exp_merge)
+
+
 if __name__ == "__main__":
     main()
diff --git a/qp_pacbio/util.py b/qp_pacbio/util.py
new file mode 100644
index 0000000..d6d1143
--- /dev/null
+++ b/qp_pacbio/util.py
@@ -0,0 +1,39 @@
+# -----------------------------------------------------------------------------
+# Copyright (c) 2025--, The Qiita Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+from os import environ
+from os.path import join, expanduser
+from configparser import ConfigParser
+
+from qiita_client import QiitaClient
+
+
+plugin_details = {'name': 'qp-pacbio',
+                  'version': '2025.9',
+                  'description': 'PacBio processing'}
+
+
+def client_connect(url):
+    name = plugin_details["name"]
+    version = plugin_details["version"]
+
+    config = ConfigParser()
+    conf_dir = environ.get(
+        "QIITA_PLUGINS_DIR", join(expanduser("~"), ".qiita_plugins")
+    )
+    conf_fp = join(conf_dir, f"{name}_{version}.conf")
+
+    with open(conf_fp, "r", encoding="utf-8") as conf_file:
+        config.read_file(conf_file)
+
+    qclient = QiitaClient(
+        url,
+        config.get("oauth2", "CLIENT_ID"),
+        config.get("oauth2", "CLIENT_SECRET"),
+        config.get("oauth2", "SERVER_CERT"),
+    )
+    return qclient
diff --git a/runner.py b/runner.py
index 5b4f73f..bcb9eb1 100644
--- a/runner.py
+++ b/runner.py
@@ -6,12 +6,8 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
-from configparser import ConfigParser
-from os import environ
-from os.path import expanduser, join
-
-from qp_pacbio.qp_pacbio import generate_sample_list, generate_templates
-from qiita_client import QiitaClient
+from qp_pacbio.qp_pacbio import generate_sample_list, pacbio_generate_templates
+from qp_pacbio.util import client_connect
 
 import click
 from subprocess import run
@@ -26,28 +22,6 @@
 QIITA_URL = "https://qiita.ucsd.edu"
 
 
-def client_connect(url):
-    name = plugin_details["name"]
-    version = plugin_details["version"]
-
-    config = ConfigParser()
-    conf_dir = environ.get(
-        "QIITA_PLUGINS_DIR", join(expanduser("~"), ".qiita_plugins")
-    )
-    conf_fp = join(conf_dir, f"{name}_{version}.conf")
-
-    with open(conf_fp, "r", encoding="utf-8") as conf_file:
-        config.read_file(conf_file)
-
-    qclient = QiitaClient(
-        url,
-        config.get("oauth2", "CLIENT_ID"),
-        config.get("oauth2", "CLIENT_SECRET"),
-        config.get("oauth2", "SERVER_CERT"),
-    )
-    return qclient
-
-
 @click.command()
 @click.option("--artifact_id", help="artifact id", required=True)
 @click.option("--out_dir", help="output directory", required=True)
@@ -59,10 +33,9 @@ def sbatch(args):
 
     qclient = client_connect(QIITA_URL)
     njobs = generate_sample_list(qclient, artifact_id, out_dir)
-    generate_templates(out_dir, job_id, njobs)
+    pacbio_generate_templates(out_dir, job_id, njobs)
     print(qclient.artifact_and_preparation_files(artifact_id))
 
-    jid0 = sbatch(["sbatch", "--parsable", f"{out_dir}/step-0/step-0.slurm"])
     jid1 = sbatch(["sbatch", "--parsable", f"{out_dir}/step-1/step-1.slurm"])
     jid2 = sbatch(
         [
@@ -119,7 +92,7 @@ def sbatch(args):
         ]
     )
 
-    submitted = [jid0, jid1, jid2, jid3, jid4, jid5, jid6, jid7]
+    submitted = [jid1, jid2, jid3, jid4, jid5, jid6, jid7]
     print("Submitted jobs: " + ", ".join(submitted))