diff --git a/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/.dockstore.yml b/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/.dockstore.yml
new file mode 100644
index 0000000000..802ff1c1de
--- /dev/null
+++ b/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/.dockstore.yml
@@ -0,0 +1,13 @@
+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /host-or-contamination-removal-on-long-reads.ga
+  testParameterFiles:
+  - /host-or-contamination-removal-on-long-reads-tests.yml
+  authors:
+  - name: Paul Zierep
+    orcid: 0000-0003-2982-388X
+  - name: "B\xE9r\xE9nice Batut"
+    orcid: 0000-0001-9852-1987
diff --git a/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/CHANGELOG.md b/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/CHANGELOG.md
new file mode 100644
index 0000000000..2bef198049
--- /dev/null
+++ b/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/CHANGELOG.md
@@ -0,0 +1,5 @@
+# Changelog
+   
+## [0.1] yyyy-mm-dd
+   
+First release.
diff --git a/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/README.md b/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/README.md
new file mode 100644
index 0000000000..45aeb3ec82
--- /dev/null
+++ b/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/README.md
@@ -0,0 +1,21 @@
+# Host or Contamination removal on long-reads
+
+The extraction of microbiome DNA or RNA is usually contaminated by host and human DNA or RNA (but also other contaminant). It is an important to get rid of all host/contamination sequences and to only retain microbiome sequences, both in order to speed up further steps and to avoid host/contamination sequences compromising the analysis.
+
+This workflow takes Nanopore fastq(.gz) files and executes the following steps:
+1. Mapping of the reads against a reference genome of the host or contaminant (e.g. human) using **Minimap 2**,
+2. Filtering of the generated BAM using **BAMtools** and **Samtools** to keep only the reads that do not align,
+3. Generation of mapping statistics using **QualiMap**,
+2. Aggregation of the mapping statistics using **MultiQC**
+
+## Input Datasets
+
+- A list of datasets corresponding to reads in `fastqsanger` or `fastqsanger.gz` format.
+- Reference genome
+- Profile for mapping
+
+## Output Datasets
+
+- A list of datasets corresponding to unmapped reads in `fastqsanger` or `fastqsanger.gz`.
+- A list of reports of QualiMap for each sample that could be used as inputs for extra MultiQC
+- MultiQC report of the mapping statistics in HTML
\ No newline at end of file
diff --git a/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/host-or-contamination-removal-on-long-reads-tests.yml b/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/host-or-contamination-removal-on-long-reads-tests.yml
new file mode 100644
index 0000000000..05c71ec7d6
--- /dev/null
+++ b/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/host-or-contamination-removal-on-long-reads-tests.yml
@@ -0,0 +1,183 @@
+- doc: Test outline for host-or-contamination-removal-on-long-reads
+  job:
+    Long-reads:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: Spike3bBarcode10
+        location: https://zenodo.org/record/12190648/files/collection_of_all_samples_Spike3bBarcode10.fastq.gz
+        filetype: fastqsanger.gz
+      - class: File
+        identifier: Spike3bBarcode12
+        location: https://zenodo.org/record/12190648/files/collection_of_all_samples_Spike3bBarcode12.fastq.gz
+        filetype: fastqsanger.gz
+    Host/Contaminant Reference Genome (long-reads): hg38
+    Profile of preset options for the mapping (long-read): map-pb
+  outputs:
+    qualimap_stats:
+      element_tests:
+        Spike3bBarcode10:
+          elements:
+            genome_results:
+              asserts:
+                has_text:
+                  text: "Spike3bBarcode10"
+                has_text:
+                  text: "3,209,286,105 bp"
+            coverage_across_reference:
+              asserts:
+                has_text:
+                  text: "#Position (bp)"
+                has_n_lines:
+                  value: 854
+            coverage_histogram:
+              asserts:
+                has_text:
+                  text: "Number of genomic locations"
+                has_n_lines:
+                  value: 7
+            genome_fraction_coverage:
+              asserts:
+                has_text:
+                  text: "#Coverage (X)"
+                has_n_lines:
+                  value: 151
+            duplication_rate_histogram:
+              asserts:
+                has_text:
+                  text: "#Duplication rate"
+                has_text:
+                  text: "104.0"
+            homopolymer_indels:
+              asserts:
+                has_text:
+                  text: "#Type of indel"
+                has_text:
+                  text: "polyN"
+            insert_size_across_reference:
+              asserts:
+                has_size:
+                  value: 0
+            insert_size_histogram:
+              asserts:
+                has_size:
+                  value: 0
+            mapped_reads_clipping_profile:
+              asserts:
+                has_text:
+                  text: "#Read position (bp)"
+                has_text:
+                  text: "6.161988"
+            mapped_reads_gc-content_distribution:
+              asserts:
+                has_text:
+                  text: "#GC Content (%)"
+                has_n_lines:
+                  value: 100
+            mapped_reads_nucleotide_content:
+              asserts:
+                has_text:
+                  text: "16.666666"
+            mapping_quality_across_reference:
+              asserts:
+                has_text:
+                  text: "Filtered Reads"
+                has_n_lines:
+                  value: 854
+            mapping_quality_histogram:
+              asserts:
+                has_text:
+                  text: "#Mapping quality"
+                has_n_lines:
+                  value: 41
+        Spike3bBarcode12:
+          elements:
+            genome_results:
+              asserts:
+                has_text:
+                  text: "Spike3bBarcode12"
+                has_text:
+                  text: "3,209,286,105 bp"
+            coverage_across_reference:
+              asserts:
+                has_text:
+                  text: "#Position (bp)"
+                has_n_lines:
+                  value: 100
+            coverage_histogram:
+              asserts:
+                has_text:
+                  text: "Number of genomic locations"
+                has_n_lines:
+                  value: 4
+            genome_fraction_coverage:
+              asserts:
+                has_text:
+                  text: "#Coverage (X)"
+                has_n_lines:
+                  value: 51
+            duplication_rate_histogram:
+              asserts:
+                has_text:
+                  text: "#Duplication rate"
+                has_text:
+                  text: "119.0"
+            homopolymer_indels:
+              asserts:
+                has_text:
+                  text: "#Type of indel"
+                has_text:
+                  text: "polyN"
+            insert_size_across_reference:
+              asserts:
+                has_size:
+                  value: 0
+            insert_size_histogram:
+              asserts:
+                has_size:
+                  value: 0
+            mapped_reads_clipping_profile:
+              asserts:
+                has_text:
+                  text: "#Read position (bp)"
+                has_text:
+                  text: "2.273913"
+            mapped_reads_gc-content_distribution:
+              asserts:
+                has_text:
+                  text: "#GC Content (%)"
+                has_n_lines:
+                  value: 100
+            mapped_reads_nucleotide_content:
+              asserts:
+                has_text:
+                  text: "16.666666"
+            mapping_quality_across_reference:
+              asserts:
+                has_text:
+                  text: "Filtered Reads"
+                has_n_lines:
+                  value: 854
+            mapping_quality_histogram:
+              asserts:
+                has_text:
+                  text: "#Mapping quality"
+                has_n_lines:
+                  value: 37
+    multiqc_html_report:
+      asserts:
+        has_text:
+          text: "Spike3bBarcode10"
+        has_text:
+          text: "Spike3bBarcode12"
+    samtools_fastx:
+      element_tests:
+        Spike3bBarcode10:
+          asserts:
+            has_text:
+              text: "@0a0c4d2c-291f-46a4-87d5-625efbfed6a0"
+        Spike3bBarcode12:
+          asserts:
+            has_text:
+              text: "@0a0c4e88-893a-4284-9119-ab4274e05445"
\ No newline at end of file
diff --git a/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/host-or-contamination-removal-on-long-reads.ga b/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/host-or-contamination-removal-on-long-reads.ga
new file mode 100644
index 0000000000..3a960d9ffb
--- /dev/null
+++ b/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/host-or-contamination-removal-on-long-reads.ga
@@ -0,0 +1,454 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "This workflow takes Nanopore fastq(.gz) files and runs Minimap2 to map the reads against a reference genome (human, by default). It filters the output to keep only the unmapped reads and generates mapping statistics that are aggregated into a MultiQC report.",
+    "comments": [],
+    "creator": [
+        {
+            "class": "Person",
+            "identifier": "https://orcid.org/0000-0003-2982-388X",
+            "name": "Paul Zierep"
+        },
+        {
+            "class": "Person",
+            "identifier": "https://orcid.org/0000-0001-9852-1987",
+            "name": "B\u00e9r\u00e9nice Batut"
+        }
+    ],
+    "format-version": "0.1",
+    "license": "MIT",
+    "release": "0.1",
+    "name": "Host or Contamination removal on long-reads",
+    "readme": "# Host or Contamination removal on long-reads\n\nThe extraction of microbiome DNA or RNA is usually contaminated by host and human DNA or RNA (but also other contaminant). It is an important to get rid of all host/contamination sequences and to only retain microbiome sequences, both in order to speed up further steps and to avoid host/contamination sequences compromising the analysis.\n\nThis workflow takes Nanopore fastq(.gz) files and executes the following steps:\n1. Mapping of the reads against a reference genome of the host or contaminant (e.g. human) using **Minimap 2**,\n2. Filtering of the generated BAM using **BAMtools** and **Samtools** to keep only the reads that do not align,\n3. Generation of mapping statistics using **QualiMap**,\n2. Aggregation of the mapping statistics using **MultiQC**\n\n## Input Datasets\n\n- A list of datasets corresponding to reads in `fastqsanger` or `fastqsanger.gz` format.\n- Reference genome\n- Profile for mapping\n\n## Output Datasets\n\n- A list of datasets corresponding to unmapped reads in `fastqsanger` or `fastqsanger.gz`.\n- A list of reports of QualiMap for each sample that could be used as inputs for extra MultiQC\n- MultiQC report of the mapping statistics in HTML",
+    "report": {
+        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+    },
+    "steps": {
+        "0": {
+            "annotation": "Reads not mapping to this reference genome will be kept.",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Reads not mapping to this reference genome will be kept.",
+                    "name": "Host/Contaminant Reference Genome (long-reads)"
+                }
+            ],
+            "label": "Host/Contaminant Reference Genome (long-reads)",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "left": 0,
+                "top": 0
+            },
+            "tool_id": null,
+            "tool_state": "{\"multiple\": false, \"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "b88baf2c-7b71-414c-9840-3365a6bb8a27",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "1": {
+            "annotation": "Long-reads as a collection of fastqsanger(.gz) files",
+            "content_id": null,
+            "errors": null,
+            "id": 1,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Long-reads as a collection of fastqsanger(.gz) files",
+                    "name": "Long-reads"
+                }
+            ],
+            "label": "Long-reads",
+            "name": "Input dataset collection",
+            "outputs": [],
+            "position": {
+                "left": 0,
+                "top": 160
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\", \"fields\": null}",
+            "tool_version": null,
+            "type": "data_collection_input",
+            "uuid": "380f0855-f80f-4dc0-a9df-9e93db63186b",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "2": {
+            "annotation": "Each profile comes with the preconfigured settings mentioned in parentheses. You can customize each profile further in the indexing, mapping and alignment options sections below. If you do not select a profile here, the tool will use the per-parameter defaults listed in the below sections unless you customize them.",
+            "content_id": null,
+            "errors": null,
+            "id": 2,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Each profile comes with the preconfigured settings mentioned in parentheses. You can customize each profile further in the indexing, mapping and alignment options sections below. If you do not select a profile here, the tool will use the per-parameter defaults listed in the below sections unless you customize them.",
+                    "name": "Profile of preset options for the mapping (long-read)"
+                }
+            ],
+            "label": "Profile of preset options for the mapping (long-read)",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "left": 0,
+                "top": 300
+            },
+            "tool_id": null,
+            "tool_state": "{\"multiple\": false, \"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "b765c0c9-10b8-4395-8bd6-7b3141489c00",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "3": {
+            "annotation": "Map the reads against a reference genome and output the ones not mapping the reference genome",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2",
+            "errors": null,
+            "id": 3,
+            "input_connections": {
+                "fastq_input|analysis_type_selector": {
+                    "id": 2,
+                    "output_name": "output"
+                },
+                "fastq_input|fastq_input1": {
+                    "id": 1,
+                    "output_name": "output"
+                },
+                "reference_source|ref_file": {
+                    "id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Map with minimap2",
+                    "name": "fastq_input"
+                },
+                {
+                    "description": "runtime parameter for tool Map with minimap2",
+                    "name": "fastq_input"
+                },
+                {
+                    "description": "runtime parameter for tool Map with minimap2",
+                    "name": "reference_source"
+                }
+            ],
+            "label": "minimap2",
+            "name": "Map with minimap2",
+            "outputs": [
+                {
+                    "name": "alignment_output",
+                    "type": "bam"
+                }
+            ],
+            "position": {
+                "left": 300,
+                "top": 140
+            },
+            "post_job_actions": {
+                "HideDatasetActionalignment_output": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "alignment_output"
+                }
+            },
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy2",
+            "tool_shed_repository": {
+                "changeset_revision": "6945cd53bd2d",
+                "name": "minimap2",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": {\"__class__\": \"ConnectedValue\"}}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"BAM\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"cached\", \"__current_case__\": 0, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2.28+galaxy2",
+            "type": "tool",
+            "uuid": "b43a7f78-e9d5-49ab-98c9-070514036269",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "4": {
+            "annotation": "Generation of mapping statistics",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0",
+            "errors": null,
+            "id": 4,
+            "input_connections": {
+                "input1": {
+                    "id": 3,
+                    "output_name": "alignment_output"
+                }
+            },
+            "inputs": [],
+            "label": "QualiMap",
+            "name": "QualiMap BamQC",
+            "outputs": [
+                {
+                    "name": "raw_data",
+                    "type": "input"
+                },
+                {
+                    "name": "output_html",
+                    "type": "html"
+                }
+            ],
+            "position": {
+                "left": 561.8009561567164,
+                "top": 126.87561946128731
+            },
+            "post_job_actions": {
+                "HideDatasetActionoutput_html": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "output_html"
+                },
+                "HideDatasetActionraw_data": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "raw_data"
+                }
+            },
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0",
+            "tool_shed_repository": {
+                "changeset_revision": "30a201c9c310",
+                "name": "qualimap_bamqc",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"duplicate_skipping\": \"0\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"per_base_coverage\": false, \"plot_specific\": {\"n_bins\": \"400\", \"paint_chromosome_limits\": true, \"genome_gc_distr\": null, \"homopolymer_size\": \"3\"}, \"stats_regions\": {\"region_select\": \"all\", \"__current_case__\": 0}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2.3+galaxy0",
+            "type": "tool",
+            "uuid": "ff81b1f0-47ef-4a70-b23b-a009aeb0711b",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": "qualimap_stats",
+                    "output_name": "raw_data",
+                    "uuid": "7df71ec2-03a9-4385-9a24-d57b2ad3360d"
+                }
+            ]
+        },
+        "5": {
+            "annotation": "Split BAM into mapped and unmapped",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_mapped/bamtools_split_mapped/2.5.2+galaxy2",
+            "errors": null,
+            "id": 5,
+            "input_connections": {
+                "input_bam": {
+                    "id": 3,
+                    "output_name": "alignment_output"
+                }
+            },
+            "inputs": [],
+            "label": "Split BAM",
+            "name": "Split BAM by reads mapping status",
+            "outputs": [
+                {
+                    "name": "mapped",
+                    "type": "bam"
+                },
+                {
+                    "name": "unmapped",
+                    "type": "bam"
+                }
+            ],
+            "position": {
+                "left": 600,
+                "top": 370
+            },
+            "post_job_actions": {
+                "HideDatasetActionmapped": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "mapped"
+                },
+                "HideDatasetActionunmapped": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "unmapped"
+                }
+            },
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_mapped/bamtools_split_mapped/2.5.2+galaxy2",
+            "tool_shed_repository": {
+                "changeset_revision": "fa7b5520ae53",
+                "name": "bamtools_split_mapped",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"input_bam\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2.5.2+galaxy2",
+            "type": "tool",
+            "uuid": "56141fe0-3b82-4005-8035-9369f30511d5",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "6": {
+            "annotation": "Prepare QualiMap stats for MultiQC",
+            "content_id": "__FLATTEN__",
+            "errors": null,
+            "id": 6,
+            "input_connections": {
+                "input": {
+                    "id": 4,
+                    "output_name": "raw_data"
+                }
+            },
+            "inputs": [],
+            "label": "Flatten collection",
+            "name": "Flatten collection",
+            "outputs": [
+                {
+                    "name": "output",
+                    "type": "input"
+                }
+            ],
+            "position": {
+                "left": 838.3582089552239,
+                "top": 78.05970149253731
+            },
+            "post_job_actions": {},
+            "tool_id": "__FLATTEN__",
+            "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"join_identifier\": \"_\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.0.0",
+            "type": "tool",
+            "uuid": "0b98eb14-0255-4f48-8497-4f7f9d97bc35",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": "QualiMap mapping statistics",
+                    "output_name": "output",
+                    "uuid": "1944f8cc-e22e-4dec-a8da-325bb3165e8b"
+                }
+            ]
+        },
+        "7": {
+            "annotation": "Extractions of FastQ from the unmapped reads",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.21+galaxy0",
+            "errors": null,
+            "id": 7,
+            "input_connections": {
+                "input": {
+                    "id": 5,
+                    "output_name": "unmapped"
+                }
+            },
+            "inputs": [],
+            "label": null,
+            "name": "Samtools fastx",
+            "outputs": [
+                {
+                    "name": "output",
+                    "type": "fasta"
+                }
+            ],
+            "position": {
+                "left": 900,
+                "top": 390
+            },
+            "post_job_actions": {
+                "RenameDatasetActionoutput": {
+                    "action_arguments": {
+                        "newname": "Reads without host or contamination reads"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "output"
+                }
+            },
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.21+galaxy0",
+            "tool_shed_repository": {
+                "changeset_revision": "9038311ed624",
+                "name": "samtools_fastx",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"copy_arb_tags\": null, \"copy_tags\": false, \"exclusive_filter\": [\"256\", \"2048\"], \"exclusive_filter_all\": null, \"idxout_cond\": {\"idxout_select\": \"no\", \"__current_case__\": 0}, \"inclusive_filter\": null, \"input\": {\"__class__\": \"ConnectedValue\"}, \"output_fmt_cond\": {\"output_fmt_select\": \"fastqsanger\", \"__current_case__\": 0, \"default_quality\": null, \"output_quality\": false, \"ilumina_casava\": false}, \"outputs\": \"other\", \"read_numbering\": \"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.21+galaxy0",
+            "type": "tool",
+            "uuid": "2e9642e7-4404-4d9b-9530-912c62a7a665",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": "samtools_fastx",
+                    "output_name": "output",
+                    "uuid": "1a82e66c-24c1-43f9-9c3c-121bdb895f74"
+                }
+            ]
+        },
+        "8": {
+            "annotation": "Aggregation of the mapping statistics for all samples",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3",
+            "errors": null,
+            "id": 8,
+            "input_connections": {
+                "results_0|software_cond|input": {
+                    "id": 6,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool MultiQC",
+                    "name": "image_content_input"
+                }
+            ],
+            "label": "MultiQC",
+            "name": "MultiQC",
+            "outputs": [
+                {
+                    "name": "html_report",
+                    "type": "html"
+                },
+                {
+                    "name": "stats",
+                    "type": "tabular"
+                }
+            ],
+            "position": {
+                "left": 1078.5173740671642,
+                "top": 129.26367916277985
+            },
+            "post_job_actions": {
+                "HideDatasetActionstats": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "stats"
+                },
+                "RenameDatasetActionhtml_report": {
+                    "action_arguments": {
+                        "newname": "MultiQC HTML report"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "html_report"
+                }
+            },
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3",
+            "tool_shed_repository": {
+                "changeset_revision": "31c42a2c02d3",
+                "name": "multiqc",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"image_content_input\": {\"__class__\": \"RuntimeValue\"}, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"qualimap\", \"__current_case__\": 20, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"title\": \"Host/Contamination Removal\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.27+galaxy3",
+            "type": "tool",
+            "uuid": "9bfa844d-9fee-4589-8568-80070c6c6479",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": "multiqc_html_report",
+                    "output_name": "html_report",
+                    "uuid": "62e6de76-2033-413e-9f5c-7f97a3e1741d"
+                }
+            ]
+        }
+    },
+    "tags": [
+        "microbiome",
+        "contamination",
+        "long_reads"
+    ],
+    "uuid": "3af8ce70-dc73-42c1-9d20-1107f84c5395",
+    "version": 9
+}
\ No newline at end of file
diff --git a/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/plnmotmptestjob4912th98.json b/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/plnmotmptestjob4912th98.json
new file mode 100644
index 0000000000..edb9b7bb9b
--- /dev/null
+++ b/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/plnmotmptestjob4912th98.json
@@ -0,0 +1 @@
+{"Long-reads": {"class": "Collection", "collection_type": "list", "elements": [{"class": "File", "identifier": "Spike3bBarcode10", "location": "https://zenodo.org/record/12190648/files/collection_of_all_samples_Spike3bBarcode10.fastq.gz", "filetype": "fastqsanger.gz"}, {"class": "File", "identifier": "Spike3bBarcode12", "location": "https://zenodo.org/record/12190648/files/collection_of_all_samples_Spike3bBarcode12.fastq.gz", "filetype": "fastqsanger.gz"}]}, "Host/Contaminant Reference Genome (long-reads)": "hg38", "Profile of preset options for the mapping (long-read)": "map-pb"}
\ No newline at end of file
diff --git a/workflows/microbiome/host-contamination-removal/host-contamination-removal-short-reads/.dockstore.yml b/workflows/microbiome/host-contamination-removal/host-contamination-removal-short-reads/.dockstore.yml
new file mode 100644
index 0000000000..f91dcc645a
--- /dev/null
+++ b/workflows/microbiome/host-contamination-removal/host-contamination-removal-short-reads/.dockstore.yml
@@ -0,0 +1,13 @@
+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /host-or-contamination-removal-on-short-reads.ga
+  testParameterFiles:
+  - /host-or-contamination-removal-on-short-reads-tests.yml
+  authors:
+  - name: Paul Zierep
+    orcid: 0000-0003-2982-388X
+  - name: "B\xE9r\xE9nice Batut"
+    orcid: 0000-0001-9852-1987
diff --git a/workflows/microbiome/host-contamination-removal/host-contamination-removal-short-reads/CHANGELOG.md b/workflows/microbiome/host-contamination-removal/host-contamination-removal-short-reads/CHANGELOG.md
new file mode 100644
index 0000000000..2bef198049
--- /dev/null
+++ b/workflows/microbiome/host-contamination-removal/host-contamination-removal-short-reads/CHANGELOG.md
@@ -0,0 +1,5 @@
+# Changelog
+   
+## [0.1] yyyy-mm-dd
+   
+First release.
diff --git a/workflows/microbiome/host-contamination-removal/host-contamination-removal-short-reads/README.md b/workflows/microbiome/host-contamination-removal/host-contamination-removal-short-reads/README.md
new file mode 100644
index 0000000000..929664e4a2
--- /dev/null
+++ b/workflows/microbiome/host-contamination-removal/host-contamination-removal-short-reads/README.md
@@ -0,0 +1,18 @@
+# Host or Contamination removal on short-reads
+
+The extraction of microbiome DNA or RNA is usually contaminated by host and human DNA or RNA (but also other contaminant). It is an important to get rid of all host/contamination sequences and to only retain microbiome sequences, both in order to speed up further steps and to avoid host/contamination sequences compromising the analysis.
+
+This workflow takes paired-end Illumina fastq(.gz) files and executes the following steps:
+1. Mapping of the reads against a reference genome of the host or contaminant (e.g. human) using **Bowtie 2**
+2. Aggregation of the mapping reports using **MultiQC**
+
+## Input Datasets
+
+- A list of paired datasets corresponding to paired-end reads in `fastqsanger` or `fastqsanger.gz` format.
+- Reference genome
+
+## Output Datasets
+
+- A list of paired datasets corresponding to paired-end reads without the reads mapping to the reference genomes, in `fastqsanger` or `fastqsanger.gz`.
+- List of `JSON` reports of Bowtie2 for each sample that could be used as inputs for extra MultiQC
+- MultiQC report of the mapping statistics in HTML
\ No newline at end of file
diff --git a/workflows/microbiome/host-contamination-removal/host-contamination-removal-short-reads/host-or-contamination-removal-on-short-reads-tests.yml b/workflows/microbiome/host-contamination-removal/host-contamination-removal-short-reads/host-or-contamination-removal-on-short-reads-tests.yml
new file mode 100644
index 0000000000..7e7e5034d0
--- /dev/null
+++ b/workflows/microbiome/host-contamination-removal/host-contamination-removal-short-reads/host-or-contamination-removal-on-short-reads-tests.yml
@@ -0,0 +1,34 @@
+- doc: Test outline for Host-or-Contamination-removal-on-short-reads
+  job:
+    Short-reads:
+      class: Collection
+      collection_type: list:paired
+      elements:
+      - class: Collection
+        type: paired
+        identifier: pair
+        elements:
+        - class: File
+          identifier: forward
+          location: https://zenodo.org/records/15089018/files/MAG_reads_forward.fastqsanger.gz
+          filetype: fastqsanger.gz
+        - class: File
+          identifier: reverse
+          location: https://zenodo.org/records/15089018/files/MAG_reads_reverse.fastqsanger.gz
+          filetype: fastqsanger.gz
+    Host/Contaminant Reference Genome: hg38full
+  outputs:
+    multiqc_html_report:
+      asserts:
+        has_text:
+          text: "pair"
+        has_text:
+          text: "Bowtie"
+    bowtie2_mapping_statistics:
+      element_tests:
+        pair:
+          asserts:
+            has_text:
+              text: "9462 reads"
+            has_n_lines:
+              value: 15
\ No newline at end of file
diff --git a/workflows/microbiome/host-contamination-removal/host-contamination-removal-short-reads/host-or-contamination-removal-on-short-reads.ga b/workflows/microbiome/host-contamination-removal/host-contamination-removal-short-reads/host-or-contamination-removal-on-short-reads.ga
new file mode 100644
index 0000000000..46da67999f
--- /dev/null
+++ b/workflows/microbiome/host-contamination-removal/host-contamination-removal-short-reads/host-or-contamination-removal-on-short-reads.ga
@@ -0,0 +1,299 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "This workflow takes paired-end Illumina fastq(.gz) files and runs Bowtie to map the reads against a reference genome (human, by default) and keep only the reads that do not align. MultiQC is used to aggregate the mapping reports.",
+    "comments": [],
+    "creator": [
+        {
+            "class": "Person",
+            "identifier": "https://orcid.org/0000-0003-2982-388X",
+            "name": "Paul Zierep"
+        },
+        {
+            "class": "Person",
+            "identifier": "https://orcid.org/0000-0001-9852-1987",
+            "name": "Bérénice Batut"
+        }
+    ],
+    "format-version": "0.1",
+    "license": "MIT",
+    "release": "0.1",
+    "name": "Host or Contamination removal on short-reads",
+    "readme": "# Host or Contamination removal on short-reads\n\nThe extraction of microbiome DNA or RNA is usually contaminated by host and human DNA or RNA (but also other contaminant). It is an important to get rid of all host/contamination sequences and to only retain microbiome sequences, both in order to speed up further steps and to avoid host/contamination sequences compromising the analysis.\n\nThis workflow takes paired-end Illumina fastq(.gz) files and executes the following steps:\n1. Mapping of the reads against a reference genome of the host or contaminant (e.g. human) using **Bowtie 2**\n2. Aggregation of the mapping reports using **MultiQC**\n\n## Input Datasets\n\n- A list of paired datasets corresponding to paired-end reads in `fastqsanger` or `fastqsanger.gz` format.\n- Reference genome\n\n## Output Datasets\n\n- A list of paired datasets corresponding to paired-end reads without the reads mapping to the reference genomes, in `fastqsanger` or `fastqsanger.gz`.\n- List of `JSON` reports of Bowtie2 for each sample that could be used as inputs for extra MultiQC\n- MultiQC report of the mapping statistics in HTML",
+    "report": {
+        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+    },
+    "steps": {
+        "0": {
+            "annotation": "Short-reads as a paired-end collection of fastqsanger(.gz) files",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Short-reads as a paired-end collection of fastqsanger(.gz) files",
+                    "name": "Short-reads"
+                }
+            ],
+            "label": "Short-reads",
+            "name": "Input dataset collection",
+            "outputs": [],
+            "position": {
+                "left": 0,
+                "top": 0
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\", \"fields\": null}",
+            "tool_version": null,
+            "type": "data_collection_input",
+            "uuid": "f0ca536e-1255-4b44-8fad-73adec33ff74",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "1": {
+            "annotation": "Reads not mapping to this reference genome will be kept.",
+            "content_id": null,
+            "errors": null,
+            "id": 1,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Reads not mapping to this reference genome will be kept.",
+                    "name": "Host/Contaminant Reference Genome"
+                }
+            ],
+            "label": "Host/Contaminant Reference Genome",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "left": 0,
+                "top": 140
+            },
+            "tool_id": null,
+            "tool_state": "{\"multiple\": false, \"validators\": [], \"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "af636432-a9d2-4b0f-ba42-5eaa1cbe750a",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "2": {
+            "annotation": "Map the reads against a reference genome and output the ones not mapping the reference genome",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1",
+            "errors": null,
+            "id": 2,
+            "input_connections": {
+                "library|input_1": {
+                    "id": 0,
+                    "output_name": "output"
+                },
+                "reference_genome|index": {
+                    "id": 1,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Bowtie2",
+                    "name": "library"
+                },
+                {
+                    "description": "runtime parameter for tool Bowtie2",
+                    "name": "reference_genome"
+                }
+            ],
+            "label": "Bowtie2",
+            "name": "Bowtie2",
+            "outputs": [
+                {
+                    "name": "output_unaligned_reads_l",
+                    "type": "fastqsanger"
+                },
+                {
+                    "name": "output_unaligned_reads_r",
+                    "type": "fastqsanger"
+                },
+                {
+                    "name": "output",
+                    "type": "bam"
+                },
+                {
+                    "name": "mapping_stats",
+                    "type": "txt"
+                }
+            ],
+            "position": {
+                "left": 310,
+                "top": 0
+            },
+            "post_job_actions": {
+                "HideDatasetActionoutput": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "output"
+                },
+                "HideDatasetActionoutput_unaligned_reads_l": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "output_unaligned_reads_l"
+                },
+                "HideDatasetActionoutput_unaligned_reads_r": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "output_unaligned_reads_r"
+                },
+                "RenameDatasetActionmapping_stats": {
+                    "action_arguments": {
+                        "newname": "Bowtie2 mapping statistics"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "mapping_stats"
+                }
+            },
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1",
+            "tool_shed_repository": {
+                "changeset_revision": "d5ceb9f3c25b",
+                "name": "bowtie2",
+                "owner": "devteam",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"simple\", \"__current_case__\": 0, \"presets\": \"no_presets\"}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"unaligned_file\": true, \"aligned_file\": false, \"paired_options\": {\"paired_options_selector\": \"no\", \"__current_case__\": 1}}, \"reference_genome\": {\"source\": \"indexed\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"sam_options\": {\"sam_options_selector\": \"no\", \"__current_case__\": 1}, \"save_mapping_stats\": true, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2.5.3+galaxy1",
+            "type": "tool",
+            "uuid": "4f0ed86e-4ab8-4737-a980-41405a6c5295",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": "bowtie2_mapping_statistics",
+                    "output_name": "mapping_stats",
+                    "uuid": "76c58935-0b96-4549-8ff4-bd17952c903f"
+                }
+            ]
+        },
+        "3": {
+            "annotation": "Take two collections and create a paired collection from them.",
+            "content_id": "__ZIP_COLLECTION__",
+            "errors": null,
+            "id": 3,
+            "input_connections": {
+                "input_forward": {
+                    "id": 2,
+                    "output_name": "output_unaligned_reads_l"
+                },
+                "input_reverse": {
+                    "id": 2,
+                    "output_name": "output_unaligned_reads_r"
+                }
+            },
+            "inputs": [],
+            "label": "Create a paired collection",
+            "name": "Zip collections",
+            "outputs": [
+                {
+                    "name": "output",
+                    "type": "input"
+                }
+            ],
+            "position": {
+                "left": 620,
+                "top": 0
+            },
+            "post_job_actions": {
+                "RenameDatasetActionoutput": {
+                    "action_arguments": {
+                        "newname": "Reads without host or contaminant reads"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "output"
+                }
+            },
+            "tool_id": "__ZIP_COLLECTION__",
+            "tool_state": "{\"input_forward\": {\"__class__\": \"ConnectedValue\"}, \"input_reverse\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.0.0",
+            "type": "tool",
+            "uuid": "63e069fd-7c6d-48e1-b891-9ad0a93a5516",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": "contamination_filtered_reads",
+                    "output_name": "output",
+                    "uuid": "02423350-1d61-4be2-a743-9dca7bae63b8"
+                }
+            ]
+        },
+        "4": {
+            "annotation": "Aggregation of the mapping statistics for all samples",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3",
+            "errors": null,
+            "id": 4,
+            "input_connections": {
+                "results_0|software_cond|input": {
+                    "id": 2,
+                    "output_name": "mapping_stats"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool MultiQC",
+                    "name": "image_content_input"
+                }
+            ],
+            "label": "MultiQC",
+            "name": "MultiQC",
+            "outputs": [
+                {
+                    "name": "html_report",
+                    "type": "html"
+                },
+                {
+                    "name": "stats",
+                    "type": "tabular"
+                }
+            ],
+            "position": {
+                "left": 620,
+                "top": 240
+            },
+            "post_job_actions": {
+                "HideDatasetActionstats": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "stats"
+                },
+                "RenameDatasetActionhtml_report": {
+                    "action_arguments": {
+                        "newname": "MultiQC HTML report"
+                    },
+                    "action_type": "RenameDatasetAction",
+                    "output_name": "html_report"
+                }
+            },
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3",
+            "tool_shed_repository": {
+                "changeset_revision": "31c42a2c02d3",
+                "name": "multiqc",
+                "owner": "iuc",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"image_content_input\": {\"__class__\": \"RuntimeValue\"}, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"title\": \"Host Removal\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.27+galaxy3",
+            "type": "tool",
+            "uuid": "c982928f-6392-4608-a8c7-88046300a4b1",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": "multiqc_html_report",
+                    "output_name": "html_report",
+                    "uuid": "62e6de76-2033-413e-9f5c-7f97a3e1741d"
+                }
+            ]
+        }
+    },
+    "tags": [
+        "microbiome",
+        "contamination",
+        "short_reads"
+    ],
+    "uuid": "0fc16104-af45-48b0-bec5-6540e3dc2114",
+    "version": 10
+}
\ No newline at end of file